China visa issue after traveling to Taiwan

I flew from China to Taiwan a while back. I have an extend-able visa to Taiwan. Upon arrive in Guangzhou, I was informed I needed a Chinese visa to visit to Taiwan (which if you are up-to-date with cross-strait relations, isn't surprising). After making a stink, they forced me to take a Chinese entry visa and let me through to my gate. However, they refused to stamp an exit stamp as I left, so according to them, I am technically still in China (about 4 months past due). I flew to Hong Kong a month ago and made it in fine.

Since Hong Kong is a special administrative region, I'm not sure if their immigration authorities are connected. I need to apply for a Chinese visa here soon.

So, now to my question. I have two options; try and use my current passport as is, or get a new passport. If I made it into Hong Kong, does anyone know if I can make it into China? If I can then I can get the visa on my current passport. But, I would rather not show up to the consulate first and ask for a visa if they are going to deny me because of 'overstaying.'