I did the ff. tweaks for a Win 8.1 HP 64-bit PC with USB 2.0 and 3.0, SATAIII, one SSD for the boot, and two regular HDs for data around a month ago:
Selected SSD properties and enabled write-caching.
Reset page file to an internal HD.
Moved temporary folder to the internal HD.
Disabled page indexing for SSD.
Reset caches for the browsers (Cyberfox and IE) to the internal HD.
Set the session store for Cyberfox to 5 min (from 15 sec).
Made sure TRIM was enabled.
Made sure that AHCI was enabled.
Turned off hibernate.
Ran SSD tweaker and Intel SSD Toolbox and accepted tweaks, but maintained prefetch/superfetch following the latter. Set superfetch service to manual.
Set search service to manual.
and everything ran fine until a few days ago, when I tried to copy folders of MP3s to a micro SD card using a Transcend card reader. The file transfer speed would start at around 12 MB/s then drop to 0 after less than a minute, then speed up again after a minute or so. Meanwhile, several windows would freeze. It happened in both the USB 3.0 and 2.0 slots. I don't remember experiencing this when I used the reader for the first time.
I experimented by using a laptop with a regular HD and an internal card reader. The copying proceeded smoothly at around 4 MB/s with both the internal and the Transcend card reader.
I am currently copying using the same PC but with a cheap card reader. It's not as bad, with the speed dropping to 0 after a minute or so, and then speeding up again.
I'd like to know if this has anything to do with any of the SSD tweaks I made, and whether or not I should just revert to the default state, following an article I read yesterday stating that these tweaks are not needed for Win 8.1 or later.