Hi MitchellU,
Since high speed continuous is working in Auto mode that indicates a setting in Manual mode is preventing the full continuous high speed shots. If reduce flicker, Dual Pixel RAW, Servo AF, or silent shooting are enabled when you are in M mode it will reduce how many continuous shots you can get.
If the issue continues we would recommend resetting the settings on the camera. To do that put the camera into either P, Tv, Av, or M and press the Menu button. Go to the sixth page under the yellow wrench icon, select Clear All Camera Settings, and choose Okay. Once you've done that go to the sixth page under the Custom Functions tab, select Clear All Custom Function (C.Fn), and choose Okay. Once both of those setting types are cleared it will reset the camera to factory default settings. At that point check to see if the same thing is happening.
