Have tyou tried using medial player and then switching the audio to EAR PIECE to see if that is working OK?
I cant see what might have changed when you HARD RESET your device unless you had some other third party application also installed but now since you reset back to original manufactures settings this application is no longer installed.
Just a couple of other comments....why dont you change your ROM to a WM6.5 or even the latest WM6.5.5? they offer some improvements over the WM6.1. Check out here (Make sure this is your device) hxxp://forum.xda-developers.com/forumdisplay.php?f=440
for the "How to change ROMS" if you are interested.
Regarding the AudioRoute installation I cant beleive that it is anything major stopping it from working, try re routing the audio on a couple of different applications. then also make sure that you are switching the Audio in SKYPE only AFTER you have connected the call.
Finally I collected a few bits of information from around the WEB and adapted a MORTSCRIPT to allow automatic routing of the Audio (Using AudioRoute 1.2.020). This alleviates the need for you to switch the audio once the call connects. However you do need to either minimise SKYPE and then open it again to full screen in order to switch the audio. Or simply use your Volume UP button which on HTC will effectively minimise SKYPE and then bring it back to the main screen and thus switch the audio in the process!
If you are interested to get it to work then check out my post on SKYPE Forum at hxxp://forum.skype.com/index.php?showtopic=547631
The simpler method would only require the installation of MORTSCRIPT, AUDIOROUTE and a short cut on your TODAY screen to the Mortscript file which would then launch SKYPE. Therefore no need to install G-Profile (but this does give the most automated approach but will cost you for the software).
By minimising and then re opening SKYPE this switches the audio to the Ear Piece and back again to the rear speaker when SKYPE is minimised again. As the MortScript is monitoring the open window until SKYPE is finally CLOSED.