Hi Michal Heller,
Did you made code customization? If you have made code customization then your site will be messed up. If you have added css in your additional css section then activate free themes first. Copy all css that you have added in additional css section and again activate wp portfolio pro and paste all css that you have added in free version.
If you still have any issue let us know. Please post your topic on related forum group Wp Portfolio Premium
Thank you!