Several things could be going on. Based on the question as originally written you might have been experiencing buffer congestion. When the buffer is full the camera must wait until enough space has been sufficiently cleared from the buffer as the data is written to the memory card before it can take the next frame. Under such conditions, the "double tap" then pause is normal behavior.

Some things you can try to stretch the buffer further:

• Save your images as jpegs instead of raw .cr2 files. The smaller size of the jpegs allow them to be written to the CF card much more quickly. With versions 1.xx.xx of the 7D firmware, the buffer will fill after about 15 shots. By contrast, the buffer won't fill until around 94 large/Fine jpegs have been taken. Versions 2.xx.xx of the 7D firmware, released in 2012, increase the buffer to around 23 raw shots and 110 jpegs.

• Update your 7D to the latest firmware version, currently 2.0.5. You can find and download the latest versions of all of the software that came with your camera on the software disc at Canon's support page for the 7D. Version 2.x is a significant improvement over version 1.x in terms of drive speed and buffer capacity/performance.

• Use a faster memory card. Using a UDMA CF card increases the buffer performance to 15 raw/126 jpeg (firmware versions 1.xx.xx) or 25 raw/130 jpeg images (firmware versions 2.xx.xx).

If buffer congestion isn't the problem (you've since indicated you are saving your files in jpeg format), it could be an issue related to autofocus hunting. Set the focus to the desired distance and then flip your lens' AF/M switch to M for manual. That still doesn't account for the frames taken faster than what you have set the camera for, though.

You've already indicated you are setting the shutter speed, aperture, and ISO manually to allow consistency from frame to frame. For consistent color from frame to frame I would suggest also setting white balance manually. Set it either as a specific color temperature such as 5200ºK which may also be fine tuned with the WB Shift menu item, using the Custom White Balance menu item, or even designing a custom Picture Style. You can use the Picture Style software editor included in the software disc that came with your camera to have even greater control over color correction and other items and then import your custom picture style to your camera.

Edit: Now that you've also indicated you are manually focusing about the only thing left are the ways in which you are trying to get your camera to shoot the time lapses. Consider using a stand alone wired shutter release with built in intervalometer that attaches to your camera via the N3 port. I've had good success with this one purchased over three years ago.