It's definitely possible that there's a glitch =n=; If you look in C:/Users/[name]/AppData/Local/Retrace (or similar...Doing that off the top of my head), you should find a file called retrace.save. If you email that to contact@spiderlilystudios.com, I can check if something's gone wrong with the variables internally.
That said, if all the gems are lit up, your next step *should* be to check the middle pedestal...
I'm glad you're enjoying it, though! Thank you for playing! ^u^