I have no Adobe products on my iMac, never have. I used to have the Flash Player, but I dumped that a long long time ago. Flash will still play, under Chrome. It is possible that some applications do something that messes up Apple's USB software, but I think it is a problem with how Apple handles sleep and USB hardware initialization. That stuff is hard to get right and clearly they broke it.
We have many people on this forum report PRAM reset worked, I always figure, just wait as it always works after a power cycle/restart. One person took their computer in for repair and says the replacement hardware fixed it, but I wonder how well they tested it. Yeah, maybe my 7 year old iMac has a hardware problem, but one that goes away on a power cycle or reboot? I think not. It is software. It is El Capitan.
It isn't even worth identifying a culprit anyway. SDHC cards should work. Every time. They used to work in all OS X releases since my iMac was made, until El Capitan. I don't even remember what OS version it came with.
I have had the SDHC card problem since El Capitan on my iMac and newer Mini and have reported some improvement with 10.11.4 and no change with 10.11.5. My iMac has been through a few sleep cycles since I powered it up Sunday and it is ignoring my just inserted SDHC card as expected. I'd like to think that Apple has a fix all set for whatever the next release of OS X is called.
I've seen Apple introduce and fix issues over the years. I've never seen a problem like this where something that should work doesn't and it doesn't get addressed. I am sure the fix is known, but not important enough for an out of planned release cycle correction.