I'm going to take a wild guess and say it looks like the type of output you'd get from a HT12E/PT2262
http://www.princeton.com.tw/Portals/0/Product/PT2262_5.pdf (page 7 shows the bit timing).
You can confirm this if the pulse widths are 1/4 and 3/4 of the bit period (your 1.3ms), and by how many bits/pulses are sent in a packet. At the very least it looks like it really is a PWM encoding, but as to whether it is the same as the PT2262 format I'm not sure. In your last posted screen shot, there is 25 pulses, and the PT2262 format has.. two pulses per bit, 9 address bits, 3 data bits, and a sync pulse, which gives 25 pulses.
Again I could be wrong here, but if you manage to write basic code that just converts those pulse widths to bits and spits them out a serial port, you could see which bits change depending on what buttons you hit on the remote.
I believe there is an Arduino library, "Virtual Wire" that is meant for using cheap RF modules (dumb ones that are just OOK AM or FM, no encoding) that can decode these types of formats for you. I haven't used it though, but I did write code specifically for decoding this for use with ubiquitous chinese "RF remotes". It isn't that difficult, and can be run using timer interrupts so it runs in the background of whatever task the micro is doing. Also, a version of the KEELOQ protocol, used by Microchip also has a similar PWM scheme, and I'm sure they have code for a decoder available in standard C.