Initial analysis: The new version recognizes 112 functions that the old one doesn't. The old one recognizes 504 that the new one doesn't. (And the ones I looked at really were still there.) Besides failing completely on only 12 of the 1376 functions it recognized (compared to 207 of 1768 in the old version), the new version has a slight but noticeably improved decompilation quality, as expected.
I can't help but wonder if the newly-missing functions are missing because no calls to them were recognized. It might be worth it to replace one of the larger functions with something that just calls each of them in turn.
One significant problem is with injections that jmp out to ManalinkEx.dll -
Hex Rays doesn't see the jmp back to the original address, and so doesn't decompile anything else in the function after it. (This is admittedly weird behavior to expect it to handle, though.) I don't suppose there's an option to decompile both files simultaneously? If so, it'll want ManalinkEx.dll's base address, which is 0x01000000. If not, it can probably be worked around by building an executable that calls those addresses intead of jmping to them. (It'll crash horribly if you try to run it, of course, but it should be decompilable.)