The mbralign tool has not been ported to work in the XenServer environment. The best way to get your p2v VM aligned is to use the host based tools. You'll need to create a second vhd, present it and the misaligned vhd to a second VM, create a properly aligned partition on the new vhd, then use robocopy/xcopy/etc to copy the data from one vhd to another. You'll then need to replace the misaligned vhd with the one you just created. The TR Amrita pointed out has the details on how to create an aligned vhd.
Another option you might explore is gparted (Note: NetApp does not support or endorse this). It is a bootable linux distribution that might be helpful. A customer pointed it out to me, but I haven't used it.
I have read that MBRscan works under Citrix Xenserver hosts, unlike MBRAlign does. Accordding to TR3747 I must log into dom0 in order to run MBRScan. But after log in, if I try just installing by the install command it says that is not a VMware supported version (of course, I am on a Xenserver 5.5), if I untar the file which contains the tools and do ./mbrscan file.vhd it says "Unknown format, skipping..". So, my questios is, how must that tool run on Citrix Xenserver?
Ok, now I understand your previous reply. Since I am able to raise the size of disks, I must assume that are dinamic type, and of course, snapshots and machines built from them are differencing type, so the issue is clear.
Do you know if there is a newer version of TR 3747 with complete information about xenserver?. TR 3747 seems incomplete on citrix sections, it refers to missing points or do not talk about it is suppose to do.