Test Copy
I sent the final pdf off to Ex Why Zed. They agreed to send me a test copy before going ahead with the job - as I had never used their services before and the result might have looked very different to what I had imagined.
This was a good decision...
The results that came back from the test print showed that by not setting everything up in greyscale, their batch conversion system tried to make everything that was 100/100/100/100 to 0/0/0/100 however it missed areas and caused dark patches and opacity issues.
(examples on the right).
Fixing the Issue
I contacted the printing company and they explained to me how I could go about fixing the issue. This meant taking everything I had previously done in Indesign, bringing into Greyscale file in Photoshop, and then bringing it back over to InDesign to achieve true greyscale.
The other thing they recommended that I do is use 'Black' for block colours instead of 'Registration Black'. The reason I had used this previously was to achieve a darker black when printing using the photocopiers at Uni.
(This had to be applied to EVERY spread in order to achieve the correct result).