I'll freely admit that my configuration in this matter may be a little bit weird, but this possibly affects any file operation that arcanist performs, and is probably not limited to my configuration.
To reproduce (please do this on a user account on Windows that you don't care about, I'd hate for you to mess up your own account!), open the file properties on the folder C:\Users\<username>\AppData\Roaming, go to the Location tab, and change the location to some network share in the form \\server\share\folder\ etc. You may need to log out and log in again for the change to take effect. Now run arc version --trace to get an output similar to this:
arc version --trace ARGV "c:/apps/arcanist/bin/../scripts/arcanist.php" "version" "--trace" LOAD Loaded "phutil" from "C:\apps\libphutil\src". LOAD Loaded "arcanist" from "C:\apps\arcanist\src". Config: Reading user configuration file "\\NINETALES\Homes\stwalkerster\AppData\Roaming/.arcrc"... [2016-04-13 23:44:29] EXCEPTION: (FilesystemException) File system entity 'C:\Users\stwalkerster\Projects\helpmebot\NINETALES\Homes\stwalkerster\AppData\Roaming/.arcrc' does not exist. at [<phutil>\src\filesystem\Filesystem.php:1013] arcanist(head=stable, ref.master=76ae02325dd3, ref.stable=68f4a77d42c5), phutil(head=stable, ref.master=65b877383e0e, ref.stable=a6d22b5cc662) #0 Filesystem::assertExists(string) called at [<phutil>\src\filesystem\Filesystem.php:37] #1 Filesystem::readFile(string) called at [<arcanist>\src\configuration\ArcanistConfigurationManager.php:201] #2 ArcanistConfigurationManager::readUserConfigurationFile() called at [<arcanist>\src\configuration\ArcanistConfigurationManager.php:263] #3 ArcanistConfigurationManager::readUserArcConfig() called at [<arcanist>\scripts\arcanist.php:115]
In the example above, my current working directory is C:\Users\stwalkerster\Projects\helpmebot\ and my roaming AppData folder is located at \\NINETALES\Homes\stwalkerster\AppData\Roaming.
Having traced the issue on my system, it appears that Filesystem::isAbsolutePath(...) returns false for UNC paths, and as such the current working directory is prepended to the UNC path.
The fix is probably simple - modifying the regex in the Filesystem::isAbsolutePath(...) function to /^([A-Za-z]+:)|(\\\\)/ has appeared to resolve the issue for me, but I'm unaware of what impact that will have elsewhere since this appears to be a fundamental class.