Yup, I've had the insane rapid flashing mini-map triangle as well and get it on a semi-regular basis. Perhaps Stardock sticks their programmer's under rapidly strobing lights in an attempt to get them to work faster, or decrease their insanity?
Could also possibly be due to the fact my video card is now well over four years old. (Moosetek mentions this maybe a reason why). Other graphical glitches I've noticed occasionally:
Every now and then on the colony overview tab, the little planet texture maps sometimes just appear as squares, rather than spheres.
Frozen ship appears in the bottom sqaure in map (another recent post picks up on this and CariElf linked a zip file patch).
One/two ascension crystals don't swap to logo symbol when zoomed out on main game map. IE: Some swap over to logo, other's remain as visual graphic (like the sun's).
And finally, clicked on the trade tab, clicked on the trade route map cycle [show all routes / show your routes], and the whole trade route map went blank and froze for a good minute or so. Coinicidentally, it was after this I first noticed the strobing triangle mini-map effect.