Hi,
I performed a test in our demo website and I couldn't reproduce your issue.
If I right select the "mootools" popup system, I right have a mootools popup instead of the bootstrap one.
Regarding your web page source code, the boostrap popups are still generated for the product option popups.
So I think that you still have "bootstrap" (or "inherit") configured for the popup in HikaShop.
Regards,
Jerome - Obsidev.com
HikaMarket & HikaSerial developer / HikaShop core dev team.
Also helping the HikaShop support team when having some time or couldn't sleep.
By the way, do not send me private message, use the "contact us" form instead.