In experimenting with the cheat functionality of FPSE, it seems to me the problem is in the cheat code refresh rate.
Of course most people know that these cheating methods work by changing values in memory address locations. However they don't lock the values in. So if you set something with codes (for example I was trying to modify AP gained after battles in FF7) to a specific value, when the game goes to write that value itself as it's supposed to, it will overwrite whatever you put in there with the code, and your code will appear like it's not working.
If the code is in a memory address that the game only sets once, then it won't make a difference. But, if the code is in an address whose values change frequently (like exp gained after battles, health points, or magic points), then when the game goes to update the information at that address your code will get squelched, overwritten by whatever the game was putting in that location. Most cheat programs get around this by setting an update rate where the value you entered is re-injected every X number of game frames. Sometimes you even have the option to modify the update rate yourself.
It appears to me that FPSE's cheat functionality only injects the codes when you hit apply, and then never touches it again. So lots of codes simply won't ever have the ability to work with FPSE unless a refresh ability is added. Hopefully this is something we can look forward to in future updates.
PS-I found this out by modifying AP gained after battles in FF7. When I entered the codes (8009D7DC,C350) nothing would ever happen. So I tried waiting until after the battle during the victory dance as the screen fades to black and then applied the code and it worked, however all subsequent battles did not work unless I re-applied it during the fade out after the newer battles.