Which Linux? There are well oveer 500 different distributions.
Which windows? There are a of those also.
No, I doubt that it is a partitioning issue. What you are describing is what one would expect if you installed your unknown Linux distribution on a hard drive and installed part of its bootloader to the master boot record of the internal hard drive. That is the default with most (Linux, windows, other) operating systems. You wouldn't happen to know what you did? If you didn't make any changes to the bootloader installation during the installation, I expect that is what happens.
Answers to the above questions would be a good starting point. If you are able to boot whichever Linux you are using and know how to access a terminal/konsole, do that and log in as the root user and run this command: fdisk -l(Lower case Letter L in the command) and post the output here.