Hmmm, The symptoms seem like they would be related to incongruent clocking or sample rate settings.
I have had no problems whatever recording into Logic Pro X with FW1.03 or b1.07. even along with a bunch of midi controllers that could potentially gum up the works.
If I use the FM3 as a USB interface, and turn off DAW software monitoring (FM3 as USB return and with direct monitoring of the FM3's processed guitar mixed with the USB return) it works perfect, no latency and I'm tracking in a project with 12 tracks (the buffer is 128 samples - will work at 64, haven't tried 32). It records a DI USB3/4 along with the processed guitar USB1/2, and the whole mix along with the FM3 direct guitar is monitored from Output 1 with no latency: the way it should work. In the I/O menu there is a USB return volume adjustment, so you can adjust the monitoring balance of guitar/mix, without affecting the tracking level.
FM3 also works without issue going SPDIF and analog out into a UAD Apollo 8 interface.
When I first got the FM3: did a test recording of all the FM3 outputs simultaneously: As a USB interface Output 1 USB 1/2, Output 2 USB 3/4(DI), along with the Apollo (Thunderbolt) for SPDIF and Audio Outputs 1 analog, Outputs 2 analog. All the recorded tracks line up, and there was no perceptible latency in the monitoring either from the FM3 output or via the Apollo's direct monitoring.