Could be related to what happened to the clam shell on my car. In my car's case (1997) the original drive cables covers stretched/expanded, causing the inner cable from disengaging from the drive motor on one side. This resulted in the clam shell only being raised on one side and derailing from the slide/guide track on that side.
I was fortunate to catch this before any damage happened. Often the clam shell can be twisted or kinked as well as addition damage to parts of the top mechanism.
If you can put the top in the service position (half raised) you can look under the clam shell to inspect if there are any damaged parts or if both drive cables are still attached at their ends. The original cables have smooth black plastic covers while the improved later cables have a raised hatch pattern on them. if original you may want to replace them with the later versions that are less prone to stretch.
Also look at the plastic "cup"sockets at the end of the drive rods as these are known to crack or come off allowing one side of the top to raise while the other side doesn't.
I was able to get my clam shell back into it's track, trim the original cables housing allowing the inner cable ends to fully engage in drive motor, and re syncronize both sides of the top (using a electric drill to drive one cable, to level out the position of the sides of the top)
Jerky clam shell
http://www.renntech.org/forums/index.php/topic/34516-convertible-clam-wobbling-when-raising-roof/page__p__182754__hl__top+cables__fromsearch__1#ent ry182754
Cable issue
http://sites.google.com/site/mikefocke2/thetopcables
clam shell issue
http://sites.google.com/site/mikefocke2/mikesporscheboxsterwebpages/clamshell-adjustment
Plastic cup issue
http://www.renntech.org/forums/index.php/topic/16999-plastic-ball-joint/