They've had the same PM etc. since about March - why do you think this changes anything?
It is just a gut feeling. Musharraf had the support from the military and it is now uncertain if the military will accept the new government:
1) Because the civilian govt has already illustrated its impotence by very recently promising to put the ISI under civilian control -- only to be forced into a humiliating backdown by the army, who will now keep official control and unofficial more-or-less control over ISI.
2) The ISI is ever more a law unto itself. This has dramatic consequences regarding Al-Qaeda, Afghanistan and also terrorism directed against India.
3) The Pakistani army is already fighting in the Tribal Areas, and has lost a lot of soldiers recently doing so. This, plus the recent past storming of the Red Mosque, means the trust of the populace at large in the army has now disappeared. This has bad consequences for the cities, Islamabad etc., and also for conflict with India caused by the Islamist guerillas / terrorists slipping into Kashmir.
4) The populace at large has been very badly hit by big rises in the cost of living --- caused by oil, food and seed-grain prices rising rapidly and highly. Again, this means coming huge unrest in Islamabad etc., just at the time when the army are feeling put-upon, used & abused, and have lost the cooperation of the populace.
6) The present civilian govt, with no real control over spiraling prices, no control over the army, utterly no control over the ISI, is far more concerned with protecting its MP's from being pursued in court later for corruption, embezzlement and the like. The two parties in govt are quite corrupt. They will become more so.
7) Those thinking the USA can just then intervene as they will in the Tribal Areas forget that such foreign intervention will cause a potential massive rise
in terrorism, and not just from the Tribal Areas, or the Kashmir border, or even going into Afghanistan, but also big rises in Al-Qaida sympathy and so on from the cities, from Islamabad and so on.
8) Musharref is now a spent force. He personally has also lost the trust of the army. He is no longer a quantity to be reckoned with.
9) There is no politician or army person with anywhere near the support or talent necessary to really replace Musharref
effectively. This means further breakdown, further corruption, further actions by factions (such as the ISI or the Islamist militias and terrorists).
Mene, mene, tekel upharsin.