What was your slowest shutter speed set to (and did you have 'link to canon shutter' enabled)? and what was the shutter speed of photos? (and just to make sure, you were in M mode, correct?)
(perhaps you should post a screen shot of the AETTR and/or Modified menus, and list the exposure parameters chosen for photos in the sequence)
If the shutter speed of your photos was equal to the slowest shutter speed you had set in the AETTR menu, then AETTR was behaving exactly as expected, increasing the ISO to 3200 (once shutter speed limit is hit, AETTR begins increasing ISO). You can either increase the slowest allowed shutter speed or get faster glass.
If your photos were overexposed, then you might have had the SNR limits or highlight ignore percentage set too high.
Also I want to ramp exposure using shutter speed not ISO, but instead throughout the shooting the camera just kept increasing the ISO automatically
There is no reason to not increase ISO once shutter speed limit is reached. All else equal (shutter and aperture), higher ISOs have
less noise than lower ISOs (i.e. the SNR per photon is better with higher ISOs), otherwise they would be pointless.
If you don't believe me, then take two photos of the same subject with the same shutter and aperture and different ISOs (say ISO 100 and ISO 1600). In post, adjust the exposure of higher ISO photo down to match the lower ISO photo (or vice versa) and compare the noise levels, esp. in the shadows. You will find the higher ISO shot has cleaner, less noisy shadows, but it clips to white sooner. If your ISO 100 shot was underexposed such that the ISO 1600 shot didn't clip anything (i.e. underexposed by 4 EV), then you would end up with two identical photos, except the higher ISO shot will have much cleaner shadows. Given the choice between the two, why wouldn't you pick the less noisy one (the higher ISO)?
I assume since your interval was 10s, your slowest shutter speed was probably less than that. If you were somewhere that's rather dark (i.e. not in a city with bright artificial light), once it's fully night, even an exposure of say 32", ISO 3200, f/2.8 might still be underexposed. This is why I like to use a ~45s interval for day to night timelapses with a slowest shutter of "32 (like in this example:
http://www.magiclantern.fm/forum/index.php?topic=12330.0 which hit those limits even in the presence of an almost full moon).