Alistair Darling was being hailed the new Mogadon Man, last week after his snore-athon Budget speech. But there was nothing soporific about his assault on the Scottish whisky industry. Slapping 59p on a bottle, the largest price increase since 1991, was a slap in the face for one of Scotland's biggest export success stories. It certainly woke up the Scottish Labour finance spokesman Iain Gray who described it as a "bombshell" at a CBI business breakfast.

The whisky tax will do little to stop binge drinking since neds are rarely seen with a bottle of The Macallan in their fists. Nor will it raise much revenue, since the Treasury's figures forecast falling domestic whisky sales. But it will harm sales abroad as other countries will feel entitled to slap on a similar duty.

So, why apply what the Scotch whisky producers called a "punitive" duty on the national drink? Well, it looks like another attempt to teach Scots a lesson: if you indulge yourselves by voting SNP, don't expect any favours from HM Treasury. And don't look to Labour in Westminster to protect Scotland's economic interests.

The whisky tax follows a succession of not-so-subtle attempts by Westminster to remind Scots who's boss. The withholding of £400 million in council tax benefit if the Scottish parliament votes for local income tax; the rejection of an airgun ban; the tight financial settlement last October, which gave the Scottish Executive a lower budget increase than other parts of the UK. It all looks like a latter day rough wooing.

The Scottish government's response has been muted - no threats of retaliation or angry deputations to Westminster led by the First Minister. Alex Salmond is reluctant to follow Gordon Brown's script and turn every issue into a cross-border crisis. Anyway, each time another constituency in Scotland is antagonised the nationalists can tick a box for their next election campaign. The proposal for school leavers to swear an oath of allegiance to Britain and the Queen was a unionist own goal. It will never happen but Nationalists will be able to say that Gordon Brown had considered forcing Scots to bend the knee' to the monarchy.

So, where is all this leading? Well, friction is inevitable if you have different parties in power in Westminster and Edinburgh. If it had been the Tories in power in Westminster and Labour in charge in Holyrood there would no doubt have been similar cross-border rows. But there is a particularly bitter quality to the Labour-Nat spat. Gordon Brown said during the election campaign that he "could not work with Salmond" and it may be that he is honouring his words.

The danger is that it could damage Scotland's long-term national interests.

In a declining economic environment, with recession looming and unemployment rising, HM Treasury could make life difficult for Scots. Whisky accounts for £2.5 billion in Scottish exports and thousands of jobs. Further public spending cuts seem inevitable as Alistair Darling tries to fill the hole in the UK accounts. There is little sign of any willingness to help Scotland's renewable industries, now that the UK has bet the future on nuclear power.

MSPs - and not just nationalist ones - worry that Brown may have decided upon a kind of "scorched earth" approach to Scotland; that he might exploit the coming economic downturn to show Scots how wrong they were to vote for Salmond. With the Treasury at his disposal, Brown has his fingers on Scotland's economic throat, and might be tempted to squeeze.

It would be disastrous for Labour in Scotland if voters became persuaded that Westminster was punishing Scots for voting SNP. But one very senior Labour figure told me he thought Brown had ceased behaving rationally towards Scotland. The whisky tax was a case in point - vindictive and politically self-defeating.

It all goes back to the election campaign, when the then chancellor Brown insisted on a punitive approach to the national question. Don't vote SNP, said Brown and his ministers, or you will lose the "union dividend", be thrown out of Europe, become a haven for terrorists. And just don't even THINK of more powers for Holyrood. It was patronising and even a little insulting, and it played very badly among Scottish voters.

Friends of former first minister Jack McConnell are adamant that if Brown had listened to his Scottish leadership, and mounted a more pro-Scottish campaign, Salmond would not have entered government. But he did, and Brown has to deal with it. Except he won't.

The image is of a baleful and brooding Brown, increasingly intolerant of Salmond's popularity and impatient with neo-nationalists in his own Scottish party; looking for ways to ensure that his prophecies of nationalist doom are fulfilled. The question is: where does that leave his protege, Wendy Alexander? She had a better week at First Minister's Question time, but as Labour prepares for the Scottish conference next week, there is deep unease throughout the party about her leadership. The former Labour minister Margaret Curran is not the only senior Labour figure who doubts she is up to it.

One source said that she is in denial about how badly her leadership is going down at all levels in the party.

There is a fear that she is too dependent on her direct personal link to Brown and that this is leading her to make unwise decisions, such as raising whisky taxation at question time a week before the Budget. She clearly had foreknowledge of the chancellor's intention to raise the tax on spirits and was preparing the ground for him by arguing that the Scottish government should back the tax to combat alcohol abuse. Was that wise?

If the impression gains ground that Wendy Alexander is Brown's Holyrood puppet, it will be a hard political negative. Worse, if Wendy is seen to be conniving a punitive approach to Scotland at Brown's behest she could even split the party. Scottish Labour is in a poor condition and divided over the national question. Labour MPs and UK ministers want it to be an out and out unionist party, dedicated to destroying the Nats. Others, such as those around former leaders Jack McConnell and Henry McLeish, want the party to challenge the SNP on its own territory, seeking greater autonomy for Scotland and dumping the "unionist" tag altogether.

Labour's fate hinges on the PM's mood. When he first entered Number 10, the Scottish party was jubilant. But I'm not sure how many would now be prepared to swear an oath to Gordon Brown.