How a template can affect WP-ADMIN speed?

I have a high speed quad core 32gb ram dedicated server. Front page of site is amazing fast, but wp-admin is extremely slow. After checking everything (plugins etc) I noticed that the problem occures only if I enable my template. So its a template issue. But I have made lot of changes and author cannot support me on this, as the original untouched theme works fine. So I have to find what it cause son my own. Can you give me directions what and where to look? How a template can affect the backend (wp-admin) of wordpress? What php files etc