It's all done in J2000, however if "Telescope needs local topocentric coordinates" is ON, all coordinates in and out of the telescope are precessed to and from "JNow" (which is actually a misnomer, the proper name is Local Topocentric or just Topocentric) by virtue of the USNO NOVAS Positional Astronomy algorithms. Most amateur telescopes need Local Topocentric. The options is on by default in ACP. If it were wrong, every pointing update would be off and you't know something was really wrong. I think the problem you're seeing is that the initial pointing is off. THat's a mount-dependent process. What if you left the mount powered up all the time? ACP keeps the tracking off when idle, but beware if you disconnect ACP as part of shutdown be sure the mount for some reason doesn't do an uncommanded/spontaneous startup of tracking which wooudl run it into the pier during the day.