For the record running Count Pages on 3,247 EPUBS took 19 minutes, it ran at low priority on one core and never got above 15% total CPU utilisation. When I was running it on RTF's (same books) it was appreciably slower - 15 minutes for 40 books, and its CPU utilisation was up to 98% of all 4 cores.
On the issue of the plug-in using the first format in the Input list, I now have EPUB as number 1 input, and RTF as number 2, and EPUB as the Preferred Output. I tweaked my workflow, I now delete the current EPUB immediately prior to creating a new one via conversion from RTF. Yes its on backup, besides I delete to the rubbish bin so its there too, and Windows probably has a Previous Version from last nights system checkpoint.