I believe you have a few options , or reasons for this happening.
1) If you are working directly in CMYK - in both the PDF and PSM, then I think you may have an embedded colour profile changing the colour in the PDF at RIP stage - depending on the Rip there is usually a setting to remove any embedded colour profiles.
2) If you have a spot or PMS colour in the PDF, then I would suggest also creating a spot in PSM (V6) (with exactly the same name), then allowing the RIP to do a look up and replace of that named colour - overriding any colour profiles, should give you the same colour when output in both the static PDF and variable PSM content.
3) You could also use a program such as Pitstop to adjust the PDF colour directly in Acrobat - however, again if you save with colour profiles the colour will change when printed.
4) You could also read the section in the PSM help (V6) about colour profiles - which can be enabled under preferences.
Hope this helps.