Yes sounds like there is a issue with formats if you are printing photos best to use and RGB input profile (most rips do this by default) and use perceptual render intent this will help with colors that you can not print due to CMYK ink.
Also if you have a file with a SRGB profile embbeded and you use a different input profile such as adobe rgb1998 you will have color differences also.
Do a search on color managment here on the forum there is alot to it.