Well, good to hear the fighters are fixed. As for the Garda, I'll try and explain in detail what I do to produce it. I've also PM'd you with a download link for a replay, even though I'm not entirely certain that will be helpful.
I start a new game on a random small 2-player map. Immediately construct mines, upgrade planet population and build two military research facilities as soon as the resources are available. Research the Garda, construct and send to a jump point. Once I've ordered the Garda to jump, I zoom in to the maximum possible and watch as the phase jump commences. Once it enters phase space, I can clearly observe the ship mesh blinking in and out of existence during the whole course of the jump within the bright white graphical effects of a ship traveling. If I take my cursor off the ship and put it back on, the infocard in the lower right flashes at the same frequency as the ship.
Once the Garda exits phase space, all is normal again. I didn't check it in the replay I constructed, but the other two games where I observed this, I tested all other TEC ships and none behaved in the same manner. You can zoom in and out on them during jumps and they were solid meshes with no blinking.
I'm going to go into the game later tonight and check all three races and their ships to see if any others do in fact share this problem. I could see how this could be unique to my system, but it seems rather odd that the same class of ships would do it every time. If I find others that exhibit the same behavior and you still can't reproduce it, I'll chalk it up to gremlins on this side.