Hi, simnutty2!
I'm not S3PE specialist and I haven't so much experience with 3rd parties content, I'm using this method mostly on EA packages. I think, there may be some issue with so big files - if you attempting merge more than 200 MB for final merged package(I think, it depends, how strong PC are you having). Maybe can it be out of memory error?
Check before yours packages for compatibility and eventually conflicts, then divide them in smaller groups (I have token usualy something about 170-180 MB), then after merging should it be under 200 MB.
If this don't help and if you don't obtain another help here, try to ask directly on Simlogical forums (subscription needed, but this is a safe site).
