Battery life in dual-boot HTC HD2
No, it is because at first boot (ie: inizialization), Android creates a Battery stat file to calibrate the battery.
After the first boot, you can start Android with any battery percentage.

If you think that after a long time, the battery percentage is not correctly reported, you can force Android to recreate the stats file with some root utilities available in the Market

Skype/MSN do draw a lot of battery, anyway, if you are using them from Windows Mobile, they are not running from Android.

You could try using greenpower or juicedefender to see if the data connection is the problem