Hey guys, after battling 3 days with my menu which was loading in an odd bunched up way and then spreading to the actual locations... I finally made a breakthrough. Jano at Offlajn was tweaking my Universal AJAX Live Search module and I asked him to take a quick look at my menu and see if he had any tips... he pointed out that it was an on.load javascript event and the only way to fix it was to speed up my javascript. He told me to try disabling some of the optimizations done, as some of them could slow it down rather than speed it up.
As I had JCH Optimizer Pro installed with everything enabled, I thought I had covered my ground, but while doing a YSlow I noticed how big my merged JavaScript file was... so what I did was I disabled that to have multiple smaller ones. I did keep the other settings enabled such as Minify, Compress, Gzip etc. and boom, the problem was solved!
What I am getting at is JCH Optimizer is a fantastic plugin, but if you use all the Stackideas products on the same site and have a couple of modules or a template with JS, I advice against merging all the JavaScript as in my case it slowed my site down by creating one huge file lol...
P.S. I did get a better YSlow score with it enabled, but it actually slowed it down... so take YSlow scores with a grain of salt