I just reproed it on a machine that never had Mame or CMP on it.

Steps:
1) Download CMP.zip and extract to C:\CMP
2) Download Mame096b.zip and extract MAME.EXE and XML2INFO.exe to C:\MAME (NEW VERSION)
3) Download Mame087b.zip and extract MAME.EXE and XML2INFO.exe to C:\CMP (OLD VERSION)
4) Launch CMP
5) Go into profiler and click CREATE
6) Browse to C:\MAME\MAME.EXE
7) Enter "Mame96" as description
8) CLick CreateDAT
9) Click OK
10) Click LOAD/UPDATE
11) Click OK and wait for it to finish (Note it said C:\MAME\MAME.EXE when it started)
12) Click SCANNER

Notice title of screen says "Scanner | Mame96 | 5145 / 5145 Sets (+22 BIOSSets)"

This is version 87 NOT version 96 being loaded

13) Close the scanner window
14) In windows explorer, rename the MAME.EXE at C:\CMP to "bad.exe"
15) Click PROFILER
16) Click Clear Cache
17) Click LOAD/UPDATE
18) Click OK and let it load
19) Should get an error now about wotw, click NO
20) Click Scanner

Notice title of screen now correctly says "Scanner | Mame96 | 5632 / 5632 Sets (+25 BIOSSets)"

This is now version 96 being loaded.

I can zip up the files if you need them but I think the repro steps are easy enough to do without a huge file download. Let me know if you do need the archive uploaded.