Exotic keyboard layout results in incorrect characters input

My default keyboard layout is Bépo (a French variant of dvorak).
When running autopilot tests with this keyboard layout, some characters are messed up when being input in a text field: dot (".") is incorrectly replaced by semi-colon (":"). Note that with this keyboard layout, semi-colon is obtained by pressing shift+dot.
If I use `gnome-control-center region` to set the default keyboard layout to US-qwerty, I can’t observe the issue.

Not sure if this has anything to do with the use of xmodmap, here is the output of xmodmap on my machine just in case:

osomon@granuja:~$ xmodmap
xmodmap: up to 4 keys per modifier, (keycodes in parentheses):

shift Shift_L (0x32), Shift_R (0x3e)
lock Caps_Lock (0x42)
control Control_L (0x25), Control_R (0x69)
mod1 Alt_L (0x40), Meta_L (0xcd)
mod2 Num_Lock (0x4d)
mod3
mod4 Super_L (0x85), Super_R (0x86), Super_L (0xce), Hyper_L (0xcf)
mod5 ISO_Level3_Shift (0x5c), Mode_switch (0xcb)

Note that when autopilot tests are being run, the debug output claims that it’s sending the key event for ".", but instead ":" is input:

10:49:04.102 DEBUG X11:214 - Sending press event for key: .
10:49:04.205 DEBUG X11:217 - Sending release event for key: .