I would suggest you look at the MRTG support sites for help on this. It really sounds as if you have a problem with too many perl threads running, IE, too many MRTG threads.
Removing commented-out interfaces in the files would have no benefit. I don't know how your system is configured, but it sounds as if your scheduler is kicking off one perl/MRTG instance for every .cfg file you have. This is going to be hard on your memory resources.
I've never used MRTG under windows, so I have no experience with the scripts you use to schedule it. Here, we have a custom-written perl script that spreads the retrieval over the 5-min window and controls the number of simultaneous threads - but its customised for our site, and will definitely only run under linux. I can't post a copy of it because there's no way I could make it work on a general host.
If you run MRTG under UNIX it is much more efficient since you can use the Forks: directive, and create a master .cfg that controls the data collection. I don't know how you would achieve this under Windows, though, and of course you'd not be able to use any of the automation scripts that the windows bundle includes.
You can probably get more suggestions for how to improve performance under windows from the MRTG website or maybe some other windows users here could provide a pointer?
I've moved this thread to the MRTG forum since it's not a routers2 problem.
UNIX Systems, ITSS, University of Auckland, NZ
Woe unto them that rise up early in the morning... -- Isaiah 5:11