With the alignment example loaded, Configure Keyboard Shortcuts reveals the shortcut to toggle the alignment panel.

Good news, although probably a little late for the anonymous original poster.

With the correct setup, Foldit standalone can indeed display the alignment panel.

The file example.zip contains the files example_template.pdb, example_template.template.pdb, and example_template.align.  (No idea why there are two PDB files, but I think one is the starting protein, and one is the guide shape of the alignment target.)

At startup for Foldit standalone, select "Import PDB/Fasta", then select the three "example_template" files and click Open.

Foldit will then open with a protein displayed. The default hotkey "N" (actually a lowercase "n") then displays the alignment panel and the guide shape. The "smiley face with lab goggles" icon also shows or hides the alignment panel.

I have created a wiki page for Foldit standalone which just happens to show this example. 

Just for information, there's a new version of Foldit standalone.

The game version of Foldit had major changes that were released in September 2022.

Among other things, the Windows version of Foldit is now 64-bit. There were also changes in several other areas.

While a step forward in many ways, the new version caused a certain amount of heartburn for longtime Foldit players. It's likely that any standalone users may also encounter some unexpected behavior.

I see this userecho support site has had very little traffic over the years. Worse, there have been no replies to any reported problems.

The game version of Foldit has a somewhat active user community. See https://fold.it, where you'll find the support forums under Community. One support possibility is to post a bug report in the Bugs forum. Please include "standalone" in the subject if you go that route.

Another option is to join the Foldit Discord server. See the link on the front page of the Foldit website for that. On Discord, the #bugs-and-feedback channel is another way to possibly find help. Discord is a little more user-friendly when it comes to dragging and dropping file attachments.

There's no guarantee of a response to any reported issues, but you'll probably improve your odds if you go to the game side of Foldit. 

For reference, the version information for Foldit is found under General Options (ctrl + T), on the Advanced tab. The current version of Foldit standalone is 20230109-b54c9a359c-win_x64-INTERNAL.

The game version Foldit had a major update released in September 2022. Those changes have also affected Foldit standalone.There are lots of changes to the user interface, but most of the underlying functions should be intact.

The current version of Foldit standalone is 20230109-b54c9a359c-win_x64-INTERNAL, indicating a build date of 9 January 2023. You'll find this infor under General Options (ctrl + T), on the Advanced tab.