If I were to capture my 1080i footage off an FX1 at 1920x1080 square pixels would I be keeping the resolution at maximum? Or is the footage off the FX1 only 1440x1080 with non-square pixels?

The latter. 1440x1080.

You can't capture something that's not on the tape, and the tape records 1440x1080, that's the HDV standard. But you can use software to resize the footage (VirtualDub for example).

Why would you need such a file in the first place? For computer playback? Any decent media player software should be able to read the file header that clearly states the pixel aspect ratio, so the picture should be the right format.

Why would you need such a file in the first place? For computer playback? Any decent media player software should be able to read the file header that clearly states the pixel aspect ratio, so the picture should be the right format.

Compositing reasons. It's easier to handle square pixel footage through multiple programs rather than having to tell each program individually that it's got a funky aspect ratio. A slight bother, but not a huge inconvenience. I was just curious.

Sony V1U outputs 1920x1080 uncompressed via HDMI, if you capture it live (not to tape).

FX1 also outputs uncompressed, but only via Component out (and in 4:2:0 color space vs. 4:2:2 with V1U). You can then capture that uncompressed analog signal by Blackmagic Multibridge into your PC as either uncompressed HD, or in the Cineform codec of your choice (Cineform now says they support HD-SDI cards from Blackmagic Decklink).

Here is an all-digital solution but you will need extra professional products to complete this. One way for PC based user is to use either the Sony V1 camera or the M25/1500 decks for uncompressing the HDV from 1440x1080 to 1920x1080. I am using FCS2 using a new Mac Pro to capture in real time. If you can get your hands on the V1 or M25 deck you can use the HDMI port to the Black Magic Intensity card that should work in PC's with the PCI Express slots to whatever EDL they support. As I said I only use FCS2. Another way would be to again use the Sony V1 camera or the M25/1500 decks to get to your HD-SDI capture card, but you will need the Convergent Design MI or Nano Connect to complete this conversion between the V1 or M25 (using the HDMI connection) and your HD-SDI capture card. The V1 and M25 has an on board processor to decompress the HDV into 1920x1080i 8 bit uncompressed HD. The V1 can also allow for live captures right off the sensor chips without HDV compression. It may be worth renting a deck for certain projects to take advantage of this HDMI secret.
Good Luck
Michael Palmer