No Science on recovery / paid for contracts but contracts reset

[Damus]

Good Afternoon!

Im having an odd problem with my modded KSP 0.90 install. On a new career I am able to do the first two contracts where you launch a new vehicle, and reach 5000m, complete them, return to kerbin, recover vessel and get the science and everything. After that however I pick up the Reach 22000m and Reach Space contracts, and when I complete the contracts or not, doesn't matter, when i recover the vessel it pays me for completing the contracts, but then it shows both the contracts till being unfinished, and I go no science for anything I've done, the science tab is simply grayed out, even though I should be getting 25 or so science.

I have the following mods installed;

Fine Print

Mission Controller 2

bDynamics

XTLandertron

Remote Tech

Kethane

TacLifeSupport

Extraplanetary Launchpads

Infernal Robotics

B9 Aerospace

DMagic Orbital Science

KAS

Kerbal Alarm Clock

Kerbal Engineer

RCS Build Aid

Mechjeb

Modular Rocket Systems

MKS

SCANsat

ProcFairings

Universal Storage

Flight Manager

Final Frontier

RealChute

Any help would be appreciated, Thanks