Update. I MAY have this solved. As I said above I use Easy Reminder for missed calls. That alone works for keeping the LED flashing for those.
For SMS/MMS I DISabled Easy Reminder.
In Handcent I have my Notifications settings as: Vibrate: Always; Vibrate pattern: Normal; Blink LED checked; Enable Remiders Checked; Number of Reminders, 'Keep Repeating; Reminder Interval, 15. This last setting I think is the key. I had it at 5 thinking it needed to be the same as the stock LED flash limit.
Before the changes above I would get a vibrate reminder and inconsistent LED flash after 5 min. It's entirely possible that Handcent also updated their app's handling on the TBolt since last Thursday as they have had at least 2 revisisions. Good luck and please let me know if this works for you all.