I do a bit cameras..
Sounds like AGC like Chris pointed out..
Canon offers (they finally listened to users) firmware updates that add manual audio control that stops the AGC cranking up the gain. Though this is dependant on which Canon you have as some of them haven't got firmware updates for this.
Some juice box (the competitor of beachtek) think had something that sends fake signal on other track to settle the AGC for given level.. but it's a hack and takes a channel..
Magic lantern might be a solution too.. it allows manual audio control + listening the recording while recording & can be loaded off SD card without overwriting the camera firmware...
5DmkIII has the manual audio control directly, 5DmkII may need the firmware update to do manual control .. less gain in camera the better and you may even need attenuator if too hot
When ever I shoot a film with DSLRs I don't bother touching their audio inputs and sync later (with good guide track/slates) instead with pluraleyes or use lockit timecode buddy.. these cameras are famous for breaking their main boards after HDMI connector getting yanked.. not for stressfull environments.. one guy killed the HDMI out by plugging into audio out when connectors were not labeled very good.. so watch out
And Canon still haven't come up for a solution to listen audio while recording.. magic lantern does support this but it's your risk and may not be compatible with your camera..
And by all means.. taken all these factors together & as the audio CODEC A/D converter in Canon is not that great.. use external recorder..