Interference. Whether it's radio frequencies or some other invisible magic beams it's having a hard time sensing the fob (I think the hub is in the roof near the CHSML).
With all the technology these days, especially wireless, the air would be thick with it if you could see everything that's going on.
The truck is designed a certain way. Wire bundles, antennas, and shielding are installed to maximize signal connectivity/continuity and minimize signal interference.
Once you change something all bets are off and each truck behaves differently based on the circumstances. It could be a bulb change/conversion, it could be where you park (near antennas, signal lines, etc.), or it could be you (the Owner's Manual mentions that you might get fob interference if your cell phone is close to it).
I have not had interference issues with Lasfit (neither before or after changing the settings in the BCM) but others have. Same can be said for Diode Dynamics or the laundry list of budget options on Amazon.
My last truck was a 2003 Ford that had halogen headlights and was light on shielding as none of this stuff was around when it was designed. I read of many people having interference issues when adding modifications to modernize the truck (HID headlights, wireless options, etc.) to the point where some functions didn't work including the truck would shut down as it interfered with the ECM signals (which required more modification to prevent that).
Unless you know where the issue is you don't have much choice besides live with it, keep changing bulbs until you find ones that work, try changing the brake light back to stock halogen (I hear that solves the issue for some), or change them all back to stock. I've also read a thread where someone shelled out some serious cash for the OEM LED CHSML and that worked.