What do you mean doesn't remember the settings? It had no problems applying mine, although I haven't permanently saved any. My only problem with ShanaEncoder is that it won't multithread, making it slow. VidCoder is fast, but failed on an OGG Subrip file that ShanaEncoder had no problems with. Although further testing may be needed, I feel too lazy to do so right now. Any fix for ShanaEncoder's "Multi thread/Sync"? *Nevermind, just had 50% instead of 10% CPU utilization. Dunno how it's working but it works.
It just not remembering the configurations I've made. For example, I set the CRF value to 20 but it stays on 23. Good to know it works for you anyway.