I would try some basic isolation troubleshooting. The following are not necessarily in the best order for fast isolation, rather, they're in the order I thought of them!
(1) Connect your A30 via component rather than HDMI. If this fixes the problem, you've eliminated the disc itself as the root cause. Could still be the player, the cable, or your HDTV. If it doesn't fix it, you've gained no new information.
(2) Try a friends Transformers disc in your existing setup. A different way to answer the same question as (1).
(3) Take your A30, your disc, and your HDMI cable over to a friends house and try it on their HDTV. If it works, you've isolated the problem down to your HDTV, or some interaction between your A30 and your TV.
(4) Replace your A30 with a friends player. Use your disc, HDMI cable and HDTV.
(5) If (4) still shows the problem, find a different friend with a different model of player, maybe an A2, A30, etc. Use your same disc, HDMI cable, and HDTV.
Bottom line: Try as many different combinations of disc, player, model of player, cable, connection (HDMI vs. component), and HDTV as possible - but be sure to only change ONE thing at a time, and take notes on whether the problem cleared or persisted. It is probably one thing that is the root cause of your problem, and you just need to isolate what it is. But keep in mind that it could be an interaction between two things - your player and HDTV being the most probable.
The above process will be much more fruitful if you have an unlimited number of friends, that have different models of HDDVD players, who all own the HDDVD version of Transformers, and don't mind you messing with their systems!
[ p.s. - The one big assumption in all the above is that your have a real problem. i.e., the Transformers disc normally plays for other people without the flaws you've noted. If what you're experiencing is the norm for everyone else, you can troubleshoot until you're blue in the face with zero results. I don't have Transformers on HDDVD so I can't tell you my personal experiences. ]