Here is a copy of setmode compiled for Linux Ubuntu x86 -- might be good to include the contents in your setmode.zip?
It would be good to port setmode to libftdi rather than the proprietary libftd2xx library. It should be pretty easy to port but I didn't want change too many things at once and when I got the setmode working with libftd2xx on Linux the motivation to do the porting rapidly dissipated :-P
It also seems that sigrok only works with the pipistrello in FIFO mode, even when I load the serial/uart bit streams? I'm planning on adding some code to the p-ols driver in sigrok to check for this.
Just for interest, I'm currently using sigrok+pipistrello for working on AC'97 for our FPGA SoC. AC'97 is 12MHz, so the 100MHz sample rate is useful to make sure alignment is correct and get multiple samples per bit.
I'm also interested in adding TMDS (HDMI / DVI) decoding to sigrok as part of my "tmds_encoding" stuff in the hope of getting more people understanding that protocol. Do you have any advice on getting the pipistrello to receive that? At 640x480 the pixel clock is 25.175MHz and hence will need the SERDES operating at ~1Gb/s to get 4 samples per bit (as bit clock is 10*pixel clock). This is within the range of the Spartan 6 but will require a bit of fiddling.
Tim 'mithro' Ansell TimVideos & HDMI2USB.tv