I had a somewhat similar issue the other day with Win7. Under the Win 7 recovery tools, go into the command line and use diskpart to make sure the Win7 Partition is active. Then use bootsect and bootrec to fix the mbr and such(both can be found under the default directory when you launch Command Line. X:\something\ I believe. Also for bootsect Win 7 is nt60, this will make sense when you try to use the command).
Thank you will need to restart, go back into Win 7 recovery and run the Startup Repair, after this is done you should be able to boot into W7. Then using MSconfig you should be able