This has been something that has always bugged me, and I'm not sure if its working as intended..
Every time I restart the client I have to turn the speed limiter back on - which is sometimes annoying as I forget to do it.
I know someone brought this up on the old V5 board as well (back in 2010) but the answer at that time seemed to indicate it wasn't supposed to do this..
Also as a side note.. if we had an option to control the update speed of GUI (current speed, file progress, basically anything that updates in real time) it would be nice. I tend to like my updates to come faster (500ms or so) than they are, and I think this throws off the readings on some stuff as well, as I constantly see my bandwidth peaking /bottoming out as much as 500KB/s from my actual Speed Limit. I don't have reason to believe that is actually the case, as the resource monitor shows a rather steady 3MB/s on my connection, but the program readout seems inaccurate nonetheless.
But that is a minor quibble at best. The forgetting Limiter enabled setting is my major headache.
I'm on Windows 7 x64 if that's relevant (seems the old issue poster was too), and all my other options appear to save just fine.