When you use multiple loops - like a custom loop in your side bar, it may overwrite your main loop... After troubleshooting where the problem was occurring and trying rewind_loop() unsuccessfully I found that starting a new loop would do the trick...
while (have_posts()) : the_post();
//the_content() was getting overwritten when by itself
//but when enclosed with the while() statement
//it works properly
the_content();
endwhile;
This works, but Im not sure if this is best practice, if you have any follow up suggestions feel free to post...