Error from log file:

Octokit.NotFoundException: Not Found
   at Octokit.Connection.HandleErrors(IResponse response) in C:\projects\visualstudio\submodules\octokit.net\Octokit\Http\Connection.cs:line 607
   at Octokit.Connection.<RunRequest>d__55.MoveNext() in C:\projects\visualstudio\submodules\octokit.net\Octokit\Http\Connection.cs:line 588
--- End of stack trace from previous location where exception was thrown ---
   at System.Runtime.CompilerServices.TaskAwaiter.ThrowForNonSuccess(Task task)
   at System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(Task task)
   at Octokit.Connection.<Run>d__54`1.MoveNext() in C:\projects\visualstudio\submodules\octokit.net\Octokit\Http\Connection.cs:line 573
--- End of stack trace from previous location where exception was thrown ---
   at System.Runtime.CompilerServices.TaskAwaiter.ThrowForNonSuccess(Task task)
   at System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(Task task)
   at Octokit.ApiConnection.<Get>d__8`1.MoveNext() in C:\projects\visualstudio\submodules\octokit.net\Octokit\Http\ApiConnection.cs:line 0
--- End of stack trace from previous location where exception was thrown ---
   at System.Reactive.PlatformServices.ExceptionServicesImpl.Rethrow(Exception exception)
   at System.Reactive.ExceptionHelpers.ThrowIfNotNull(Exception exception)
   at System.Reactive.Subjects.AsyncSubject`1.GetResult()
   at GitHub.InlineReviews.Services.PullRequestSessionManager.<StatusChanged>d__19.MoveNext() in C:\projects\visualstudio\src\GitHub.InlineReviews\Services\PullRequestSessionManager.cs:line 224
{"message":"Not Found","documentation_url":"https://developer.github.com/v3/pulls/#get-a-single-pull-request"}
2018-02-15 10:26:34.600 INFO [01] GitHubPackage             Initializing GitHub Extension v2.4.2.1331 in Microsoft Visual Studio 2015 (14.0.25420.1)
2018-02-15 10:26:58.338 EROR [01] PullRequestSessionManager Error changing repository
System.InvalidOperationException: An attempt was made to transition a task to a final state when it had already completed.
   at System.Threading.Tasks.TaskCompletionSource`1.SetResult(TResult result)
   at GitHub.InlineReviews.Services.PullRequestSessionManager.<StatusChanged>d__19.MoveNext() in C:\projects\visualstudio\src\GitHub.InlineReviews```

On https://github.com/github/VisualStudio/tree/fixes/1493-wrong-repo I added some logging. I then created two shortcuts to run the experimental instance: one to open github/VisualStudio and one to open haacked/Rothko.

Clicking on the first shortcut (github/VisualStudio) followed by the second (haacked/Rothko) reproduced the bug. Here is the log produced:

2018-02-16 15:48:33.059 INFO [01] GitHubPackage             Initializing GitHub Extension v2.4.3.0 in Microsoft Visual Studio 2015 (14.0.25420.1)
2018-02-16 15:48:34.486 DBUG [01] VSGitExt                  ActiveRepositories changed to []
2018-02-16 15:48:34.488 DBUG [01] VSGitExt                  Found IGitExt service and initialized VSGitExt
2018-02-16 15:48:34.492 DBUG [17] VSGitExt                  IGitExt.ActiveRepositories (#43546682) returned ["C:\\Users\\grokys\\Source\\Repos\\VisualStudio"]
2018-02-16 15:48:34.965 DBUG [15] VSGitExt                  IGitExt.ActiveRepositories (#43546682) returned ["D:\\projects\\Rothko"]
2018-02-16 15:48:37.004 DBUG [15] VSGitExt                  ActiveRepositories changed to ["https://github.com/editor-tools/Rothko"]
2018-02-16 15:48:37.004 DBUG [17] VSGitExt                  ActiveRepositories changed to ["https://github.com/github/VisualStudio"]
2018-02-16 15:48:37.389 DBUG [15] TeamExplorerContext       ActiveRepository changed to https://github.com/editor-tools/Rothko @ D:\projects\Rothko
2018-02-16 15:48:37.391 DBUG [17] TeamExplorerContext       ActiveRepository changed to https://github.com/github/VisualStudio @ C:\Users\grokys\Source\Repos\VisualStudio

You can see that IGitExt fires with the change notifications in the correct order, but on different threads. By the time VSGitExt.ActiveRepositories is set, these two notifications are out of order.

Nice spelunking there, good work!