What triggers "time gems" in lightning-mode?
I just watched this GDC talk by Jason Kapalka (Co-founder and chief creative officer at Pop-Cap), where he talks about Bejeweled. It's a very interesting and entertaining talk btw., so have a look at it.
Around 48:30, he answers a question regarding A.I. and he says that apart from the fact that the A.I. will make sure you always have a possible move (in modes where that matters), there is no sophisticated A.I.
Earlier in the talk he also mentioned that a huge part of Bejeweled is simply based on luck. So this (and playing lightning-mode a lot), leads me to the conclusion that the "time gems" are triggered randomly and there's no A.I. or special moves that will increase their rate. It boils down to luck.
Update: Of course you get more time-gems if you can clear lots of gems faster (especially using power-gems) because more new gems entering the board also means more "time gems".