Actually, I think the product is very fit for purpose. I regularly run over 100 markets in a row, with a reasonably sized trigger (50kb) on the fastest mode. If I set up the TM properly, it runs through smoothly. If it slows down, it is generally that I have not set it up very well, changed the triggers or performed some other action. Once I get it going, off it goes and it doesn't stop until it is supposed to stop. Occasionally, there may be a very slight difference in bets matched particularly on the first market as it may not be fully in tune with the trigger yet. But in terms of an overall strategy developer, records maker or database builder I am unaware of anything else that comes close.
Missing an individual bet or two on a TM run may well happen as you say, but in real mode on BF as an experienced trader yourself you know it will happen even more often.
So I would advise you to persist until you perfect your method. When you notice a particular market repeatedly freezing, perhaps re-download that market from BF and try again. If you have any specific problems, post them up and most probably someone will have the solution for you.
Best of luck
Larp