I'm assuming you tried clearing media storage like it says in that link? have you tried going into recovery, wiping cache/dalvik and rebooting?
for now, you should be able to move your media back onto your phone by mounting the phone as disk drive when you plug it into the computer, yes? if for some reason that isn't working, download airdroid from the market and you can transfer files wirelessly
oops. just read what isyncr is. does it only work with mtp? I see they have a wireless add on...that should be the same as airdroid, but airdroid is free. but really wiping the data from media storage and then your caches should probably fix it
edit #2: you said this stopped working after you rooted; is usb debugging still enabled? one of the comments on the market says to try disabling that...