Colors change / Colors not the same / PDF's get cropped after saving/re-open

First Off I'm using Ai CC, file mode CMYK and I work within the same file, I do not place colors into a different file.

I'm making different panels for a vehicle wrap, I work within the root file (CMYK) and I save out of the root file as a PDF, so everything is done within the same file with the same color. The first instance I had a group of files lets say 100, 89, 8 ,1, after the file was saved I re-opened it and the colors changed to 100, 88, 11, 1 and some files from the same group stayed the same??

Second instance working within the same parameters as above with a different color 60, 13, 25, 0, (teal) again all made working in the same root file, after print there were 2 different colors of teal, re-opeded the file and the numbers were the same, so I though it was a print issue, but when I re-saved under a different name, it printed out correct, and to test it, I took the more pale teal version and placed it in the brighter teal file, it printed out right, even though they were made from the exact same root file, and saved out of that root file.

So, why if these two separate files, made from the same root file, same color mode, same CMYK numbers, saved as the same extension have different info embedded in them after saving and re-opening?