@substring
Will try a Samsung 128GB FIT USB 3.0 (MUF-128BB/AM) after I back everything up.

I'm okay with linux, I can use it daily and not freak out. I could hdparm and report back, I doubt the speeds are the problem though. Let me know what you need, I'll try my best.

@Pepe
Yes, both are running 4.1.0-master-pi3-2017-03-23

I've run into a strange problem with loading time after upgrading my SD card from 32GB to 128GB. Oddly it's only with N64 . Load times on the 32GB card are between instant to about 5 seconds. On the 128GB card load times are between 20 to 30 seconds. Load times for every other system are fine, just the N64.

The only hardware change would be the SD cards, both are UHS-I / Class 10 and both have pretty much the same read/write speeds.
32GB Read Speed 80MB/s Write Speed 15MB/s
128GB Read Speed 80MB/s Write Speed 20MB/s

I followed the Noobs guide for the 128GB card with guiformat. https://github.com/recalbox/recalbox-os/wiki/Installation-(EN)

I figured I'd search/ask here what could be the problem and what's the best course of action to remedy the situation. Long loads a terrible. Should I reformat using a different method? Is this a problem with SDXC cards vs SDHC? Could it just be my card and should I buy a different one? Any advice is appreciated, thanks.

Raspberry Pi model: Pi 3 Model B
Recalbox version (build) : 4.1.0-master-pi3-2017-03-23
Micro SD: Team 32GB microSDHC(TUSDH32GUHS03) / Team 128GB microSDXC(TUSDX128GUHS03)
Power Supply: 5v 2.5A Micro USB DSM-0525 w/inline vampire switch
Controller: logitech f310