Perfect Dark 64 Save Issues

[Scope32]

Just the other day I ran into my first major issue with PD 64 on Project 64. I created a Save State at the mission debriefing of "Escape A51", but every time I click the "Accept" button the mission accomplished music just keeps on playing and it never loads the "Escape A51" mission. Until this point I had never had issues loading levels.

After doing a lot of searching on the interwebs I decided to try using Mupen64 to see if it could get past this problem; however, you cannot load save states between different emulators (as far as I know). Of course, the .eep files work fine as long as you add the " (U) [!]" business to the Project64 files before trying to open them in Mupen. I can get Mario64 and Majora's Mask to load their .eep files on Mupen from PJ64, but the PD64 .eep file appears to not have any of the save data on it.

So I have several questions:
1) Why does my PD64 .eep file appear to have no saved data on it?
2) Is there a way to do a manual in-game save of PD64 (like talking to the owl statues in Majora's Mask) or does it just auto-save the stuff as you complete missions? And if it does auto-save, then I revert to question 1.

Finally, whenever I try to switch my agent profile in PD64 (hoping that this would create an automatic save when leaving my main profile), I get the following N64 message when trying to access my main profile again: "Error Loading Game -- Game Pak -- The saved file has been erased due to corruption or damage -- Cancel". This happens every time I choose my main agent profile, in which case I just revert to my save state, otherwise that profile is completely deleted.

Thanks in advance.