Comment 229 for bug 195982

For me, it turned out that the "Caps Lock as an extra control key" was the culprit. xmodmap was

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), Caps_Lock (0x42), Control_R (0x69)
mod1 Alt_L (0x40), Alt_R (0x6c), 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)

I removed the Caps_Lock (0x42) from the control line and the problem went away. VMWare stopped flushing my mappings and my keys all worked the same as before. Somehow my CapsLock is still mapped as a control key as well.