Bukkit

What steps will reproduce the problem?

Running VirtualPack with the build of Spigot I have seems to be causing some majorly high Pct Tick, which subsequently lags down the server a fair amount. It's one of several plugins that's begun to act up since the 1.7.9 update.

What version of are you using?
Bukkit: Spigot Build #1494
Vault: 1.4.1
VirtualPack: 2.7.5

Do you have an error log of what happened?

Timings: http://aikar.co/timings.php?url=4e919cd775bd49233f4bf75c5504cec7

Please provide any additional information below.

Startup logs are available upon request. There are no obvious errors, just the significant lag in that event as well as a couple of others you can see on the timings report.

This means VThreadWait ran a total of 2 times, but it took 5.5 seconds each time. Or the first run took almost no time and the second one almost 11 seconds.
It's supposed to be like the latter, because: GroupManager does not actually set up the player permissions or groups when the plugin is enabled, but delays it until some later point. This sucks for me, because my VirtualPack relies on permissions/groups being present when it loads. So what I do (if GM is present) is just delaying the loading of the whole plugin (which apparently takes ca. 11 seconds in your case). If you check your startup log, VirtualPack should take almost no time there. Instead it creates a server task to check if GroupManager is done yet, and if so, then it loads everything.
And you must have caught the last two ticks of that waiting period.

If this were what's actually causing lag (continuously), your server would tick only once every 11 seconds.
However, I still fiddled around with the VThreadWait a bit (dev build #118), running it only once every 20 ticks and setting it up a little smarter.

I tweaked some settings and got this in my timings as well:

http://aikar.co/timings.php?url=118ac1eab2161f4eea8789cd86f623ac

The only reason I suspect it has to do with VirtualPack somehow is because when I disable the plugin and run everything else exactly the same, the server runs fine - 19-20 TPS constantly even with 50 or 60 people online. I'm not sure what could be causing it.

I'll give the newest dev build a try and see what that does.

The newest dev build seems to be giving me the same issues. I'm not precisely sure what's causing it, but I'd be happy to provide any startup logs you want to see. I'm still not getting any errors.

@Islid: Go

After VirtualPack has loaded, could you run "/v ad threads" and tell me what it says or make a screenshot of it please?