Hi Emma,
Are you implying that this is an Elegance issue?
The generic term 'Bootstrap' can be confusing as it is both a theme and a framework. I think that you are implying the latter, but I think given your description that its really an Elegance issue because you say they work well in other themes, and core themes are based upon Bootstrap framework 2.3.2. See: https://moodle.org/mod/forum/discuss.php?d=312844#p1252588.
Now given that Elegance uses Bootstrap framework 3.x via using the Bootstrap theme then that would imply a fault in the theme but not really the framework because Shoehorn also uses the Bootstrap framework 3.x but now is stand alone. I've not yet tested Shoehorn in M2.9.
Now, given your description I would say that it is a JavaScript issue, therefore please see if there are any errors on the console. Also, I notice that Elegance has not been updated for M2.8 and M2.9, that Bootstrap theme is available for M2.8 but not M2.9 where there needs to be changes to make an M2.9 version: https://github.com/bmbrands/theme_bootstrap/pull/360. Therefore I suspect that there is a conflict in the loaded libraries somewhere.
What other themes have you tried?
Cheers,
Gareth