it is a well known fact...to align the VM filesystem with the VMFS ..as per the vMware official docs.. for 2003 and linux VMs with EXT3 filesystems...like RHEL5... debian 4, 5 etc.. is not aligned... you need to manually align.. the other partitions.. like the DB data.... logs etc...
just type... fdisk -lu as root...
To check that your existing partitions are aligned, issue the command:
fdisk -lu
The output is similar to:
Device boot Start End Blocks Id System
/dev/sdj1 128 167766794 83883333+ fb Unknown
Aligned partitions start at 128. If the Start value is 63 (the default), the partition is not aligned
you can also use other tools like... paragon,acronis or any partition tools from netapp...etc..to align the vm partition.
RHEL 6 aligns partition automatically. and it is aligned to 2048. and 2008 also...it is for 1024.
as per the vmware doc for linux you need to align..128...