Most partition software (free and commercial) on Windows have an option to align a partition
. Most modern operating systems and/or file-systems do this automatically. However, if you have formatted the drive in the enclosure and you use partition software to check for alignment you might see that it is out of alignment because of those 512 byte sectors. If so, alignment could help with putting the data on your disk on geographic locations that can be found if you swapped the disk from the enclosure into the computer.
I assume this type of software on Linux will have the alignment option available as well. But I'm not versed enough in Linux to tell you which application that could be. What I can tell you is that I did align every partition while I still was running XP on a 1TByte HD (cloned from a much smaller, older and dying HD) and I couldn't help but notice that the disk I/O wasn't stellar. With Process Explorer I checked the disk I/O and saw that it was almost always consuming between 0.5 to 2% of my computer resources.
After alignment it never got above 0.5% anymore and usually remained below 0.1%, something you definitely noticed in day-to-day use. Partition alignment works fast on empty partitions, but can take a very long time if a partition is crammed with data. Mine was full and it took almost 5 hours to align all partitions. However, it was worth it.
The link has a graphical representation of what the problem most likely is.