Strange issue in Volume size


I am experiencing a strange issue in windows 2008 sp1.I have two
disks(vmdks) having capacity 40gb each.One disk is Boot disk of Windows 2008
SP1 VM(say it is Source VM). while other is attached to windwos 2008 SP2
VM(say it as target VM) as normal disk.Both disks have MBR Partition style.
Each disk is containing one volume(spawning in whole disk).But I am seeing
diff volume size for both volumes.The source VM volume capcity is more than
the target volume capacity.When I ran chkdsk I found that in the target side
the total number of available blocks is less by 256 hence resulting in 1mb
loss in size(block size is 4096 bytes).I am not able to find out why this
is happening.Please help me in finding the possible cause.

Please note that I am seeing this issue for boot disk only.