I've had people have the same issue when using the Custom/CWD folder setting, so that's no good either. I've also had reports of someone having the same issue with Google Chrome in his downloads dir, and coupled with my problems in SVN sync its become pretty clear its not PCSX2 specific. The only commonality thus far: Windows 7. So I'm chalking it up to a bug in Win7 NTFS.
In order to fix your inis folder, you may need to delete all of the pcsx2 folder and run a chkdsk. (it generally won't report anything but that doesn't mean it didn't make filesystem changes -- there are some subtle consistency info updates that chkdisk does to an NTFS filesystem while its running that it doesn't verbosely talk about while doing them).
In order to fix your inis folder, you may need to delete all of the pcsx2 folder and run a chkdsk. (it generally won't report anything but that doesn't mean it didn't make filesystem changes -- there are some subtle consistency info updates that chkdisk does to an NTFS filesystem while its running that it doesn't verbosely talk about while doing them).
Jake Stine (Air) - Programmer - PCSX2 Dev Team