I think we need to clarify how this stuff works. When PHD2 is connected to the mount directly - via ASCOM in your case - 'bump' operations are routed directly to the mount through that interface. The AO never sees any of that and your ST-4 cable isn't being used. I suspect you might not believe this so here's the excerpt from the debug log file for a 'bump':
23:17:30.394 00.000 8412 starting a new bump
23:17:30.394 00.000 8412 AO travel limit exceeded, using large bump correction
23:17:30.394 00.000 8412 Scheduling Mount bump of (3.026, -8.476)
23:17:30.394 00.000 8412 ScheduleSecondaryMove(100EBFD8, x=3.03, y=-8.48, opts=4)
23:17:30.394 00.000 8412 Enqueuing Move request for scope (3.03, -8.48)
23:17:30.394 00.000 8412 move complete, result=0
23:17:30.394 00.000 8412 worker thread done servicing request
23:17:30.394 00.000 1208 Worker thread wakes up
23:17:30.394 00.000 1208 worker thread servicing REQUEST_MOVE scope ofs (3.03, -8.48) opts 0x4
23:17:30.394 00.000 8412 Worker thread wakes up
23:17:30.394 00.000 8412 worker thread servicing REQUEST_EXPOSE 2000
23:17:30.394 00.000 6728 GuideStep: -21.7 px 8 ms EAST, 22.1 px 17 ms SOUTH
In the parlance of PHD2 and AO operations, the "primary" mount is the AO driver and the "secondary" mount is the ASCOM mount driver. So the ST-4 cable shouldn't be connected and simply provides another potential source for cable snags and drags.
Given this situation, we wouldn't expect there to be any statistically meaningful difference in results between 3/24 and 4/09 unless the sky conditions were different. And that's what the data show. Your results for the 4-hour guiding session on 3/24 showed a total guiding rms of 1.25 arc-sec while the longest guiding session on 4/09 had a total guiding rms of 1.18 arc-sec - not a statistically significant difference either way. So your perception about a difference was mistaken, possibly because you're just trying to judge results in real time. That's why it's important to use the LogViewer and pay attention to the statistics over reasonably long intervals.
At this point, you should probably be focused on improving the overall results which aren't particularly good. Operationally, you need to start following all the recommended procedures: update to the latest release (2.6.14), use a dark library, bin the camera to 2x2 if possible, use the Calibration Assistant in the correct part of the sky while following all its instructions, run the Guiding Assistant, etc. Until you get the system stabilized, you should also keep your guide camera exposures at 1 second or greater.
Regards,
Bruce