I'm working on the same project I was having EQ issues with and all of a sudden there's a slight bit of delay. Nothing changed so I know the settings are the same. If I close the project and open another one it's fine. Go back to the other one it's ok for a minute and it's back.
 
The only thing I have on this project is 6 guitar tracks, multichannel out ezd drum track and the one bass track I'm playing with. No plugins on the bass track, just straight in.

It seems I have fixed it by bypassing all FX. That pretty much told me where the problem started so I just deleted a few unneeded tracks and it appears to be ok now.
 
There's not really that many FX, so is there a limit before all chaos breaks loose?

It might depend on the FX used. If you have heavy VSTs, for example such that have a look-ahead function or use heavy oversampling, the latency is more likely.  There are really big differences between VSTs in that respect. 
That's why it's often good to the heaviest ones only in the mixing phase (or freeze some tracks) when buffer size is not an issue.

Hi. What plugin(s) were on the tracks you deleted? Could be a plugin issue, and not SONAR.
Best of luck.

I used different tones from Ampltube and POD Farm to get left, right and center guitar tracks, total of 6, But the tracks I deleted were previous bass tracks I had muted. I just saved to a new project and deleted them. Those tracks had a compressor, amp sim and EQ.

If the compressor has a "look ahead" function that would probably add latency. Some are particularly bad. Freezing the tracks before muting might have solved the problem - Sonar keeps plugins on muted tracks or plugins that are "off" active in case you unmute or switch the plugin on. Otherwise audio would be interrupted while the plugin catches up,

Compressors can have "look ahead" time which basically is a manual latency slider. Limiters especially very often have this. In addition, various higher end EQs have adjustable latencies, specifically the ones that offer "linear phase" processing. The latency is needed in order to reach linear phase processing. However, most of these things should only affect latency if
A. They're on a bus, so the bus input is summed "live" during playback - meaning Sonar will need to delay other tracks to line up with the latency inducing plugs
B. They're on your live input channel, also needing Sonar to delay tracks to make up the difference.

In other cases, Sonar will compensate not by delaying the tracks without latency causing plugs, but by pulling the tracks with latency inducing plugs a little bit ahead of the other tracks, again lining up audio from various tracks.