EPSON Scan software being put to sleep?

I have the latest EPSON Scan software (3.9.4.0EN) which according to Epson is tested for El Capitan. It has always acted a little weird – failing to notice clicks sometimes unless I Cmd-Tab to the app first, for example – but under El Capitan it is exhibiting some very annoying behaviour.

I run the preview scan and select multiple frames for full scan (I'm doing 35mm negatives) and it proceeds to scan the first frame. Then, sometimes, it pauses after saving that frame. To get it going again I usually have to click on its progress window (anywhere) and it will instantly begin scanning the next frame. One time the pointer was already over the window and I just moved the mouse slightly and that woke it up after a pause of several minutes.

At one point I quit it and relaunched and it could not see the scanner at all. A power cycle on the scanner did nothing and in the end the only thing that got it to work was launching VueScan and doing a test scan before quitting that and trying EPSON Scan again.

I could put up with most of the oddities but I often leave it to scan 6 frames which takes around 10 minutes only now I will have to stay with it to keep prompting it onto each frame.

The scanner is connected to an OWC Thunderbolt 2 hub and both VueScan and Image Capture can see it first time every time.

Is this some power saving feature causing the software to sleep while it's "not in use" (i.e. not getting user input)?