I glanced through the forum and did a search, but couldn't find anything like this particular issue.
The simple explanation is as follows:
1) BizHawk creates files in a way that windows doesn't think they exist unless I run it as admin. (Even screenshots)
2) Running BizHawk as admin makes the game I'm playing with run under 40 fps, but makes the files visible to Windows.
I've checked every setting in BizHawk that I can find between the two, since running as admin uses different config files, to make sure all the options are the same, yet the unexplained slowdown from running BizHawk as admin persists.
I'm not very good at explaining this issue in detail, so have some screenshots. Running Bizhawk normally is on the left, admin is on the right.
http://i.picpar.com/BR3b.png
http://i.picpar.com/CR3b.png
http://i.picpar.com/DR3b.png
http://i.picpar.com/ER3b.png
Extra details:
-Opening up the command prompt as admin still cannot to find the files in question. It shows an empty directory. (Same goes for trying to find the files in safe mode. I tried it just because why not.)
-I tried changing the permissions on said files, but the only way to even open the properties dialogue is through BizHawk. When I actually attempt to change the permissions, Windows throws a "Windows is unable to find this file" error at me.
-Changing the priority and affinity for BizHawk seems to have no effect on the performance issue.
-I tried taking ownership of the hidden "Movies" folder that exists if I delete the Movies folder from the admin version of Bizhawk. Even taking ownership, removing the system permissions and setting everything to be fully visible and editable by the admin account, along with the option to make these changes to all subfolders and files makes no difference.
I get the idea I'm missing something simple, but I cannot search out what that simple answer might be.
Obligatory Computer details:
Windows 7 64 bit
i7 920 2.67 GHz
12 Gigs of RAM
Geforce 550Ti graphics card
Memory usage from BizHawk never seems to go above a negligible value, and watching the performance tab never shows the CPU going above 50% so I have no idea why BizHawk is running poorly as admin.