I started to experiance a slow down, couldn't get eMule to come back on the screen, and downloads were stuck. I went to the eMule folder and just happened to look at the folder under the eMule folder named Temp where I noticed that most of the files were in 3s, but some were only 2.
In some cases, the .bak file wasn't there. Just for the heck of it, I moved all the files that didn't have the 3 files to a Misc folder, restarted the eMule program and it's been working properly and faster.
The files that represented the downloads that I wanted that are now in the Misc folder will be moved back to the Temp folder later, and I'll see what happens then.