A sliver of the beginning of track 7 is cut off of blood07.ogg and instead appears at the end of blood06.ogg. I confirmed this by comparing them to tracks 6 and 7 on my Blood CD. Track 6 should end in silence.
--Edit--
blood07.ogg has a little bit of track 8 at the end. This makes me suspect others might be messed up too.
For a little more clarification:
Track 6 is 4:51, blood06.ogg is 4:52
Track 7 is 3:11, blood07.ogg is also 3:11 but still has a similar problem.
--Edit 2--
The same problem between 6 and 7 seems to exist with all tracks. Blood07.ogg seems to be the only one with even the right length.
2. 5:11 CD, 5:14 ogg
3. 7:08 CD, 7:09 ogg
4. 2:55 CD, 2:56 ogg
5. 4:36 CD, 4:37 ogg
8. 2:55 CD, 2:56 ogg
9. 2:07 CD, 2:06 ogg

Confirmed. Wondering how this happened, as the tracks on my original CD aren't run together or anything. Was it ripped in a faulty program? if so I'd recommend that they be re-ripped in something a tad more reliable, like EAC.

EAC has been much more user friendly in its more recent iterations. Please consider re-ripping the tracks using it.

Odd bug. Let's hope GOG team will fix that soon.

In the mean time, a very easy fix for this and any other problems with CD music is to open dosboxBlood.conf and go to the bottom where the following is:
c:
cls
blood.exe
exit
Add -nocd to the blood.exe line, so it reads:
c:
cls
blood.exe -nocd
exit
This will force it to use midi instead of CD music. This will not disable the cutscenes, you will still be able to see them.

Yes, and I got this answer:
Hello,
Thank you for putting this into our attention. I will look into this,
and if possible, the soundtrack will be replaced by the better one.

Well, hopefully that is a good sign.

It's because the tracks were ripped from an improperly made CD image. The original retail disc is a Mixed Mode CD which means the first track is data (game data) and the subsequent tracks are CD-DA (raw CD audio). This format was used heavily in older games (Dos, win 9x) and is notorious for being improperly imaged. Some will try and image those as an ISO 9660, which doesn't support the CD-DA so it images only the data track and disregards the audio. Others will try to rip using a non-standard proprietary cd image format (such as Nero's *.nrg) which will, in many cases produce errors just like this - where the table of contents seems to be improperly interpreted and/or implemented resulting in wrongly timed "track cuts." If this is present on a BIN/CUE image it's usually because it was previously a different type of image that was later converted to BIN/CUE or a BIN/CUE made from an improper CD-R burnt back-up.
To avoid this always rip Mixed Mode CDs in BIN/CUE or cloning (i.e. Alcohol 120%).
The good news is that this is easily fixable. The soundtrack that's included with the game (tracks 1 - 8) are the same as the CD-DA that was on the "One Unit Whole Blood" retail disc so you can just trans-code tracks 1 - 8 to OGG format and rename to overwrite the GOG ones in the game directory (i.e. Blood1-01-Pestis-Cruneto.mp3 = blood02.ogg). Since the soundtrack was encoded at 192kbps and the GOG OGG were encoded at 100kbps, it will be like an upgrade also if you encode the OGGs at 192kbps as well.

Convert lossy audio to another lossy audio doesn't sound as a good solution.
Worse thing is that damn 96kbps soundtrack. It is really stupid idea. I don't see any reason to use so horrible quality in these days. Lossless audio is not necesary for games, but this is too bad.
Why just don't use OGG with -q 6 (192kbps VBR) or -q 7 (224kbps VBR) parameters?

A 192kbps lossy re-encode of a 192kbps lossy source is way the hell better than 100kbps - especially since the 100kps default encodes are mangled. The end result is better - even if the 100kps defaults had been properly ripped.

Still not fixed?

Apparently not. Chased your support request? Maybe point them at this thread too so that they can see the suggestions.

Anyone get an ETA on this?

I'm really disappointed. This looks like GOG will not fix this bug.
Plus, 96Kbps OGG's in all redbooked GOG's games? I hope this is just a joke. I really want to buy few another games with redbook audio on GOG (Settlers 2 Gold for example), but not in this crappy quality.