Paragon Alignment Tool and Endpoint Encryption

Hello,

In an effort to make my life more bearable at work, I went out and bought a Solid State Drive to replace the hard drive in my work laptop. I figured that I would clone the existing image and would be able to do everything that I did before without having to go through my IT department to get things configured. It's a hard drive so how hard could it be, right?

So everything cloned onto the new drive fine (using a sector to sector backup), but my performance is well below what it should be. After a lot of configuration tests, I'm pretty sure that the problem is that the drive isn't aligned properly. (I even loaded XP on the drive from scratch and aligned the drive properly to prove it.) The Paragon Alignment Tool confirms this and I set it up to fix the problem but after it reboots and successfully does it's thing, the Endpoint software states that safeboot has been corrupted and the drive will no longer boot. It seems that when Paragon does it's magic it updates the MBR in such a way that Endpoint can no longer load properly to access the drive. Is this a common problem with drive encryption programs like Endpoint? I know if I go to the IT group then I'll get a lecture about how this is not a standard setup and they won't support it. I just don't have it in me to explain that all I want to do is to do my job better by not waiting forever for their horrible implementation of Windows XP to churn through what I throw at it. If I could somehow align the drive without destroying Endpoint then that would be ideal.

I know that I'm asking to somehow manipulate my company's corporate security, but I'm not looking to disable it. It's just getting in the way of better performance and it can encrypt the new aligned drive all it wants. I just want to get this laptop to fly so I don't waste time waiting at work anymore. Any ideas would be greatly appreciated!