1. Well for starters, your server is non-steam.
2. Anything with rehlds, you could edit using the game.cfg thats located in your game directory, which allows your cvars to be effective, otherwise you just have overlapping commands. I'm sure you're doing the same thing with the other cvars listed there that have designated files for them.
3. CS revo? Are these custom plugins? sql related? Do you have error logs in amxmodx/logs?
nice -n -12 ./hlds_run -game cstrike +ip xxx +port xxx +maxplayers 32 +sys_ticrate 1000.0 -pingboost 3 +map de_dust2 +servercfgfile server.cfg -master -secure
What I removed can be placed in your server cfg file as "mapchangecfgfile server.cfg" at the bottom of the file without quotes. Is your server secure? Cause then you won't need -secure if your startup has +ip instead of -ip
5. You're running a linux server. Never understood the purpose of running a pingboost when you really won't really run into those issues with linux, and it just puts a hit on your cpu, which could also explain the lag. The restart is actually necessary every few days.