Yes, the USL-1 Finals are between Canadian teams. This isn't the problem. The problems is that the USL (all levels: 1, 2, PDL, SuperY, WLeague) was purchased by a group that currently does not operate a team - NuRock Sports. They do have the rights to operate a team in Birmingham, AL and to replace the Silverbacks who did not operate in USL-1 in 2009.

The short story is that there were a few teams/owners that felt passed over by Nike when they sold to NuRock and they, through the Team Owners Association, are considering forming a break-away league. US Soccer has enough of an issue with this that Sunil Gulati is meeting with both the head of the USL and representatives from the TOA.

This is where it gets messier. Because you see the USL doesn't just have teams in the USA, but also Canada, Puerto Rico and Bermuda. Yes, even Bermuda. So while a meeting with the USSF is vital - either a resolution or recognition of the breakaway could result - it is also actually important for the USL's new owners that Canada be included in what ever decision is reached (there are 9 USL-1/PDL teams in Canada). While yes the leagues could survive without the Canadians, the Puerto Rican and Bermudans it would not be as strong. Not from a soccer standpoint, and certainly not be continuing to lose the 35 Million or so potential fans in those markets.

Let's look at some facts

Markets with the TOA -Minnesota, Miami, Carolina, Montreal, Vancouver, Tampa Bay (expansion), Atlanta (not playing this year) also not listed there is St.Louis. Basically a who's who of first and second tier soccer markets in the USA and Canada.
Markets with the USL - Charleston, Rochester, Cleveland, Austin, Portland, Ottawa (PDL to USL-1 next year)
Fencesitters - Puerto Rico, New York FC (expansion)

I’m under the impression most USL-2 clubs are with NuRock/USL. The PDL however is a different animal, with the clubs split. Keep in mind alot of the angry PDL clubs have already bailed and joined the NPSL, but I know of many others intrigued by the TOA plans and thinking about backing them.

There was even an update concerning the PDL today

We can also report that additional PDL clubs are now positioning themselves for possible alignment with the TOA, depending on this weeks developments with the USSF. So any assumption that the only clubs that are unahppy with the current structure of USL have already been accounted for publicily is incorrect.

Now, yes, some of those "breakaway" PDL clubs are the affiliates with USL-1/2 sides. But not all of them are, at least one is actually waiting to see what the MLS has to say in this whole mess.

But it gets more interesting as outside of this mess, but still lowering the value of NuRock's new property is the loss of the Hammerheads from USL-2. Yes, the Hammerheads that beat a USL-2, USL-1 and MLS side in the Open Cup this very year. That's a quality soccer side, that may not have the business acumen, but honestly belongs in a league like the USL.

For even more reading on the situation here is an interview with Carolina Railhawks President and here is more on the meeting between most concerned parties (what about Canada/PR).

MLS observers are forced to look at this and think "what does it mean for us?" There is plenty of speculation, from concepts like MLS-2, to pro/rel, to an affiliated Reserve/Farm structure to an more independent Reserve loan system. All have advantages, all would take efforts by MLS. All also depend on the failure of several soccer organizations within the related nations. The US Open Cup could shift as well, for if two leagues exist at the same level on the pyramid they'd have to have the same number of entries - wouldn't they? By the way, Real Madrid's Reserves finished 2nd in the Copa del Rey in the past and are currently in Spain's second division. German Reserve squads can qualify to play in the 3rd tier there, but cannot pass into the B-2 or Bundesliga. So there is a European analog to Reserve/Farm clubs playing within the pyramid rather than in a separate purely Reserve League.

While in the end there will be winners, soccer has a harsh history in the USA and stories like league and team failures are never a positive.

But, the major blogs aren't covering this yet (Ives, Davis, Davis, Buzz) and certainly none in the major media. To continue following this story your best sources would be Kartik Report, Triangle Offense and Inside Minnesota Soccer. The end is no where close in this saga, but like most things soccer in North America, MLS/SUM are bound to be involved.