I can't comment with a great deal of knowledge about your X3 ii firmware upgrade since I use the X5 ii, but I obviously don't have that particular upgrade and, as you see from my earlier thread, I experienced the same thing.
I can tell you that, when it came to stuttering, the Transcend card you are using did the worst of the six cards I tested on my X5. I don't want to make this entirely the fault of the card (in my mind a UHS-1 card should be ample and clearly there is a greater issue here with "unpacking" the larger FLACs), but that Transcend, at 45MB/s, does rate among the slower cards classified as UHS-1.
If no other solution is forthcoming, all I can tell you is that the Sandisk Extreme U3 64 GB (95 MB/s) performed for me with practically no stutters at all over an extended period of time and that the Lexar Professional U3 1000X 64GB (150MB/s) has had no stutters whatsoever - even with my largest 192kHz/24bit Level 8 FLACs.