You could try to upgrade the software. My father has a MiniDisc, and I too had problems with the damn thing (I still have in fact, and now I can't even get the bloody thing to work on my PC). They weren't the same as yours, though. Anyway, I use v3.4 (
http://forums.minidisc.org/downloads...ls.php?file=21, full installer, some 20MBs) on my dad's laptop and there's now v4 (
http://dl1.aii.co.jp/contents/connec...eInstaller.exe, one of those stupid installers which are only a few Kbs but then download tens of megabytes from the internet). This might help... v2 was flaky, if I remember correctly.
And don't ever, Ever, EVER manually delete the library information (stored somewhere in the Application Data folder of your user) - I did that, and now even though I re-installed a later version the damned thing will tell me that there's something wrong with the library and won't fix it. I hate Sony...
Jam it back in, in the dark.