Thanks for the file, I can now reproduce the problem.
The slowdown happens because of another packMP3 parsing error ("region size out of bounds"), opened issue #35 for that.
In commit c8dc5a0 (also see attachment), I relaxed the parsing restrictions for unsupported MP3 streams a bit. This could potentially lead to some more false positives, but most of the time, streams will be longer and the log will be less bloated. For example, for the file you uploaded:
Code:
--- Old version - 115 log entries
(13.45%) Unsupported MP3 type found at position 13440, length 3460
Type: MPEG-1 LAYER I
[...]
(13.53%) Unsupported MP3 type found at position 1505932, length 3508
Type: MPEG-1 LAYER I
--- New version - 1 log entry
(13.44%) Unsupported MP3 type found at position 4, length 1512280
Type: MPEG-1 LAYER I
This makes the log 508 lines shorter. Not that much, as it's still 87626 lines long, but a step in the right direction 
What surprised me was the time difference, did you run on a slow machine? Also which OS did you use (on Linux, Precomp sometimes seemed slower for me in the past)?
Code:
--- Your log:
New size: 106239630 instead of 52428800
Done.
Time: 31 minute(s), 48 second(s)
Recompressed streams: 896/28085
--- My log (checked with the "old" version, without the commit described above):
New size: 106239630 instead of 52428800
Done.
Time: 3 minute(s), 30 second(s)
Recompressed streams: 896/28085