Hey there! Welcome to the forum.
When I booted up my pc and clicked on the icon to open up MC, I got a pop-up window that said extracting. After it extracted whatever, another window pops up and started loading files, something similar to when you first install it.
After it finished, it said to reboot. After re-booting, I then clicked on the JR icon and it started with everything appearing to be ok.
This part is the automatic updater in MC. When it sees a new build is available, instead of bugging you about it like lots of applications, it just downloads the update. The next time you launch MC, it auto-installs it (just like how Chrome and Firefox work now). You can turn it off if you want to, but you should probably keep it turned on. It is best to have the latest MC in most cases. They release new builds most weeks, and always work in all sorts of awesome changes. If you don't want to upgrade it that often, you can set the Auto-Updater to Stable mode (that actually might be the default) and then they don't push them as often. The setting for this is under Tools > Options > Startup > Update Channels.
It shouldn't usually need to reboot the system when this happens, but it does occasionally crop up if certain components it needs to update are in-use when it runs (this seems to happen most often if you have the Shell Extensions enabled, but it isn't limited to that).
As far as your volume problems...
I know that there were some changes fairly recently with how MC handles Volume output, which might explain the change in initial volume. If it drives you nuts, you can alter it easily in the DSP. There also might have been something reset in the DSP settings between build 68 and build 99. So check your DSP settings. They messed around with a bunch of that and made it better, but your old settings might not have come out the same way on the other side.
As for the slow performance when actually changing the volume, I don't know what could be causing that. We'll need to get that figured out, but you'll need a comment from someone else.
Answer a few questions about your setup though:
1. What is Options > Audio > Output Mode set to?
2. What audio hardware are you using?
3. What do you have set in the DSP under Output Format?
4. Do you have any other crazy DSP options enabled (Convolution, Effects, EQ, Room Correction, etc)?
