When you upgrade from windows 8 to windows 8.1 it is actually a complete windows update equivalent to going from windows 7 to windows 8.
In doing so it blasts away a number of your settings that you may not have thought of.
When I installed my Samsung 830 SSD in my laptop I used Samsung magician to optimise and change the settings that are not required with SSD drives.
I did things like:
- Disabled Pre-fetch and super-fetch
- Turned off scheduled defrag
- adjusted my pagefile down to certain limit
- turn off write-cache buffer flushing
After windows 8.1 is installed all of these settings are lost. I found out much to my surprise as a defrag had been executed on my machine.
Here are a few articles that talk about all the possible optimisations, the first is from microsoft;
Windows 7 & SSD: defragmentation, SuperFetch, prefetch