OK i have figured out HOW the problem occurs you and Dumpydooby are both victims of the exact same issue...
when we Replace an existing driver in the pack We must remove all entries related to that driver from the Dosnet and Txtsetup files...
A "replacement" is what we call it when we upgrade a driver that exists natively in windows....
UNFORTUNATLY we replace a driver called ULTRA
[P8]
ms_count=1
ms_1_deviceName="Promise SATAII150 TX2plus"
ms_1_tag="ultra"
ms_1_sysFile="ultra.sys"
ms_1_hwids="PCI\VEN_105A&DEV_4d33,PCI\VEN_105A&DEV_4D69,PCI\VEN_105A&DEV_4D68,PCI\VEN_105A&DEV_4D30&SUBSYS_4D33105A,PCI\VEN_105A&DEV_0D30&SUBSYS_4D33105A,PCI\VEN_105A&DEV_4D38&SUBSYS_4D33105A"
ms_1_isBusExtender=false
ms_1_exc_replaceIfOS="wxp,w2k3"
Notice the replaceIfOS tag 
Now
Notice the lines that get deleted in your txtsetup.sif file (both of you) that are also very similar in name IE ultra*.*
ultradf3.cab = 100,,,,,,_x,,3,3
ultradf3.inf = 100,,,,,,,20,0,0
ultradfg.sif = 100,,,,,,_x,,3,3
ultradfg.sys = 100,,,,,,,4,0,0,,1,4
UltraISO.CAB = 1,,,,,,_x,,3,3
UltraISO.inf = 1,,,,,,,20,0,0
dfrg.exe = 100,,,,,,,2,0,0,ultradefrag.exe
Working on it now. I belive it has to do with nested quotation marks in the Fedit.exe routines
Obviously this only happens in 'ultra' rare cases.
IE Only if an addon Starts with same name as the replacement mass storage driver
So at least now I know:
How it happens.
What part of the code is doing it.
What triggers it.
I belive the problem is related to a really ugly set of nested quotes in a line similar to this
_runDos("""""" & @scriptDir & "\bin\Fedit.exe"" -rem -f """ & $_I386 & "\txtsetup.sif"" -s:c ""SourceDisksFiles"" -l:o """ & $NameOfDriverToReplace & """""")
working on a fix I will email you two for testing when I think i have it 