Exiftool related tags only work for the first mkv in the list?

Just upgraded to version 4 (4.05 and 4.06) and found that video (MKV) related scripts and tags that used to work in version 3 only seem to work for the first file now. As a test, I tried keeping things simple and found that even that doesn't work:

New name: <Height><Inc Nr:1>
->
With MKVs: first file works, others just show the incremented number.
With JPGs: works fine for every file.

If I delete EXIFTOOL.EXE from the aren folder then:
With MKVs: None show any height.
With JPGs: all work.

So, looks like an issue calling exiftool repeatedly?
(I tried updating exiftool from the exiftool website but then none of the MKVs work so that didn't help. I also tried using the version of exiftool from my 3.x reinstall and even that didn't work.)

Reply to #1:
The current version relies on Exiftool for MKV support. The next version (4.07) will have native support for MKV, which will help you a lot in this case.

ExifTool can be very slow at times which results in timeouts if it takes too long. If the file is large, timeout is more likely. I am working hard to add native support for as many file formats as possible, without the need for Exiftool.

Reply to #2:
I'm glad to hear that the tags might be supported natively in the next version but I think that there's something else at play here.

By opening a command prompt and running exiftool on a directory of 42 MKV files, I can see the values of every tag in under 2 second total (and I suspect that a good deal of that is just me being slow hitting stop on the stopwatch). Even if it took 2 seconds per file, it wouldn't explain how the first file always works then the others don't (I think that I read that you had allowed 8 seconds or something as a timeout value?).