I have a homebrew race (Arachnym, it's published) one of its' racial traits should allow you to pick 2 options, out of a list of 6; I added the 6 options in the "OPTIONS" tab inside the Racial Trait editor, then specified that you may pick 2 of those when creating a character by filling the "CHARACTER LEVELS WHERE OPTIONS KNOWN" with the required format: 1,1

But once I chose the race on the race editor it only allowed me to pick 1 of the 6 options. I tried to specify this happens at level 1 under "REQUIRED CHARACTER LEVEL", and even added an extra choice for testing (version 1.3) as: 1,1,1

Whenever I create a new version to test more things the "CHARACTER LEVELS WHERE OPTIONS KNOWN" section is empty, I believe this used to work before but no longer does, since I tested and edited this race a LOT before publishing it, and I doubt that this is an issue I overlooked from the begining, perhaps a problem with a recent update to the site?

This is why it is best practice to not publish until all the kinks are worked out through a period of playtesting and editing. (The issue now may be because of the multiple publications, hopefully not.) On your test character, are you switching versions of the race each time you publish a new version? The builder won’t automatically switch to the updated version for you, you have to do it manually. Are you?

Yes! I remove the old version from my collection, then I go to the Character Builder and change race (to Legacy Aaracokra usually since it's the one at the top), then I switch back to the Homebrew one. I know other changes have applied because since version 1.1 (all versions other than 1 I've made today for testing this specific issue) I changed the race's short description that appears at the top when selecting it on the creator, and that shows up just fine. The only change that doesn't seem to stick is the racial trait one.

After you save the trait, do you remember to re-save the whole race again?

Do yourself a favor and don’t publish any more versions until you get it sorted out. 

Yes! Whenever I make a change, I save on the Trait page, then go back to the Race's main page and save from there, I even go back to the specific Trait I just saved to see that I didn't imagine the past minute (the classic "manual saving" on videogames habit of going about it twice just to be sure )

Well, I know that they just did a bunch of updates to do the whole (legacy) thing, so maybe that confuzzled something. The other issue may be that one or more of the options has been incorrectly configured and that’s causing an issue. Check each option against the instructions in the Subclasses & Races FAQ #1 to make sure nothing is accidentally hinky: (https://www.dndbeyond.com/forums/dungeons-dragons-discussion/homebrew-house-rules/131411-a-homebrewers-how-to-faq).

Fixed it, I don't know which one thing may have been it, but I just tried to update everything as throughout as I could:

• Removed the race from my Collection.
• Closed the tab and opened DDB on a new one.
• Created a new version of the race.
• Removed the new version of the race from my Collection.
• Went to the Character Creator and deleted the test character.
• Closed the tab and opened DDB on a new one.
• Edited the new version of the Race to add the "1,1" under the Racial Trait's "CHARACTER LEVELS WHERE OPTIONS KNOWN" (saving, going back, and double-saving everything).
• Closed the tab and opened DDB on a new one.
• Openned the race editor to see my changes were still there (they were).
• Added the race to my Collection
• Created a new character.
• Chose the race.
• It worked.
• Published it.

The issue might've been on the character slot itself (?), since even after removing the race from my Collection the option would remain. Odd also that it would take text changes, but mechanical ones wouldn't go through. Everything I tried here I had tried before already, but not all at once, perhaps then I missed an interaction.

Thanks for the help!

A data cache must have gotten stuck on an earlier iteration for which there was no number of options entered and so it was defaulting to the base 1 @ creation. What might have also worked would have been to level the character up and back down again to force it to update its cache. But either way, it’s working now. (Huzzah!)

I’m happy to help (but I’m not sure how much I did except eliminate some of the basic troubleshooting issues from the list of what was wrong).

[Addendum]

This seems to happen when a character is left with no class chosen; after leaving the site and coming back to a character who is left at level 0: It will only allow you to pick one choice when it comes to multiple choice features. The issue seems to be in the character creator not the homebrew content, deleting the character slot and making a new one, or gaining a level in a class fixes this.

Yes, the default is a single choice at “character creation,” in order to give multiple choices the levels must be added in the correct field. But “0” is not a viable level, so you have to put “1,1” into that field. That means it cannot override the default until the character is officially “1st level” when a class is selected.