It happens recently or already been slow like that since your first 1st MUGEN'ing day please?
What MUGEN version are you using please?
Somehow MUGEN1.1 eats more computer resources than MUGEN1.0 does.
Don't know but it might have something to do with your custom MUGEN screenpack/motif, besides some heavy-duty MUGEN chars/stages you are using.........
By the way, is your Intel HD Graphics software driver updated to the latest yet please?