Not sure if this is related to this question (seems to be but I cannot comment only answer and I don't have one yet but would like to add my experience with this issue).
There are 3 foursquare apps I use on my Windows Phone. The official app, 4th & Mayor, and my own app. I've also experienced this via foursquare.com/mobile checkins.
Using the official app and my app, when I checkin to a venue, I do not show up in "Here Now" whether from phone apps or on the website or looking at the json from the API calls. When checking my "last seen at" it shows me there. Using 4th & Mayor it's hit or miss. Sometimes I'll show up in "Here Now" (within all apps and the website) and sometimes I don't.
One thing to note, when it finally does show me in "Here Now" at a venue, if I checkin to another venue and I do NOT show up in "Here Now", "Here Now" for the old venue still shows me there, so it's not clearing that out. "Last seen at" shows me in the new venue.
I'm not checking in off the grid and I do have the "Include me in the public list of people who are currently checked in at a venue" checked. Even tried unchecking it and checking it back. I've tried with 2 different accounts and I've tried with and without shouts, with and without sharing to facebook and twitter, and the normal and quick checkin options. All with the same results.
NOTE that I'm not just relying on the apps showing me that I'm at a venue, I'm looking at the raw json returned from the API, both from my app and the API Explorer @ developer.foursquare.com.
If it helps, here's the HTTP Post from my app (venue and oauth token removed):
https://api.foursquare.com/v2/checkins/add?broadcast=public,facebook&venueId=the_venue_id&oauth_token=my_token&v=20111030
I've even tried changing the version to &v=20120107 and it still doesn't work. I've also logged out everwhere I could think of and even disconnected my facebook and twitter accounts.
It is only recently this has started, within the past couple days.
So, in summary,
- When I checkin I do not show up in Here Now, either from the venues/VENUE_ID endpoint, the venues/search endpoint (I'm not counted in the here now), or the venues/VENUE_ID/herenow endpoint.
- My checkin does show up via users/self and via the checkins/recent endpoint.
Apps used: foursquare for Windows Phone, 4th & Mayor, my own Windows Phone app, and foursquare.com/mobile.