Ok so I removed the HDD from computer A and installed in computer B and its still not defragging the pagefile.sys even though in Virtual Memory settings on computer b it shows there is no page file on the E: drive but the pagefile.sys file does exist but its inactive.
Then if I defrag the E: drive with the windows tool it works fine and defrags the page file.
From what I can work out Defraggler dosn't have any detection methods for detecting page files that are inactive/in use.
If you delete pagefile.sys it will be recreated on next startup. If you have enough contiguous space it will probably be created without fragmentation.
@romanoff If done correctly there should be no unexpected behaviour the patch simply allows pagefile.sys to be processed.
I can understand your concerns about modifications and yes if you're a n00b or clueless then you should leave it alone.
As for the original problem I see no reason for pagefile.sys to be deliberately excluded I'm sure some would point out that it's locked by the Operating System, however my point is under BartPE / ERD Commander it is not locked.
For defragging pagefile.sys I use Sysinternals Contig under BartPE on many occasions and never suffered any ill effects I just wish I could do the same using Defraggler instead.