GPO Backups - Import + Merge + Export problems

Hi guys,

I've been having a weird issue with SCM that I hope you can shed some light on.

Scenario:
Via GPMC:
* Backup Group Policy A to a folder.
* Backup Group Policy B to a folder.

Via SCM
* Import Group Policy A.
* Import Group Policy B.
* Compare/Merge GPOA to GPOB.
* Merge Baselines as "Group Policy A v2"
* Export to GPO Backup (folder) "Group Policy A v2 (SCM Export)"
- Successful, but some setting were dropped "as they are were not configured". eg: 

Setting Name: NoChangingWallPaper , UI Path: Software\Microsoft\Windows\CurrentVersion\Policies\ActiveDesktop , CCEID: 
Setting Name: DisablePersonalDirChange , UI Path: Software\Microsoft\Windows\CurrentVersion\Policies\Explorer , CCEID: 
Setting Name: NoThemesTab , UI Path: Software\Microsoft\Windows\CurrentVersion\Policies\Explorer , CCEID: 
Setting Name: fEnableTimeZoneRedirection , UI Path: Software\Policies\Microsoft\Windows NT\Terminal Services , CCEID: 
+ a few more

* Import GPO Backup "Group Policy A v2 (SCM Export)" (i.e. the same one that we just exported)
* Compare/Merge "Group Policy A v2" to "Group Policy A v2 (SCM Export)"

Result:
- Settings that differ: 0
- Settings that match: 43
- Settings only in Baseline A: 28
- Settings only in Baseline B: 39

For some reason the exported GPO doesn't match the merged baseline GPO.

Version Info:
SCM v2.5.40
Software Library: v1.5.21101

I've emailed a copy of the GPMC Backups to secwish@microsoft.com, referencing this thread.

Any thoughts about why the merged, exported then imported GPO doesn't match the merged baseline?

Thanks & Regards,
Tim