Last year I had the same problem with Random Flashes, using TX, RX, EX/RX's... on LE's (v2 & v3,) MR16, OL's from RX. By the time I had everything running it was less than two weeks before pull down, so I gave up and chalked the problem up to - maybe - my Lynx Splitter. My setup was:
Dongle > Splitter > TX > LE's with EX/RX, MR16 with EX/RX, and RX > OL & LE
Dongle > Splitter > wired OL's and LE's
The Random Flashes occurred system wide and regardless of distance from the Splitter or whether a controller was wired or wireless. That's why I considered the Splitter to be the culprit.
This year, without using a Splitter, I have the same behavior, and with - so far - only one LE with EX/RX operational. The TX is high in a window 9m up, with direct line of sight to the EX/RX 12m away. The TX is a good 3m away from my pc with wired NIC, and 7m higher than the Wireless Router on the ground floor. The TX and EX/RX planes are parallel.
The Random Flashes usually occur on the "previous" channel to the one that is active; i.e. if channel 189 is on, it's channel 188 that flashes... and also usually very close to the "on" time of the active channel.
I'll play around some more with this tonight , with the first step to run a cat5 from the Dongle to the LE.