Someone else said some of this already but I'll say I found more on it too:
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On page 93 in the manual there is a note:
*In the AI Servo AF mode, the continuous shooting speed may become slightly slower depending on the subject and the lens used.
*In low-light areas or indoors, the continuous shooting speed may become slower even if a fast shutter speed is set.
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In the Troubleshooting Guide Section of the Manual - On page 245
Max burst during continuous shooting is slower:
*If you shoot a subject which has fine detail (field of grass, etc.) the file size will be larger and
the actual maximum burst will be lower than the number mentioned in the tables on page 59.
*High ISO speed noise reduction setting can cause this C.Fn II -2 [Standard/Low/Disable].
If set to [Strong], the max burst during continuous shooting will decrease. (page.208)
*When I use AV mode with flash, the shutter speed becomes slow.
-if you shoot at night when the background is dark, the shutter speed becomes slow automatically (slow-sync shooting) so that
both the subject and background are properly exposed.
If you do not want slow shutter speeds to be set,
then set C.Fn I-7: Flash sync. speed in AV mode to 1 or 2 (page 207)
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So, I wonder if the auto assist beam might help compensate and keep speeds up.
Can you test that and also the other custom function settings I mentioned?
Also, check out the -Function Availability Table- on page 237.
That table shows AE lock won’t work in Manual, but it works in P mode.
So, just configure P the way you would on Manual mode,
then test out the low light continuous shooting rate while holding AE lock!