Reproduction steps:

(1) Add utf8+w file with BOM on Linux -C1 server.

(2) Setup master Jenkins server on Linux (may not be relevant)

(3) Set up build slave on WIndows 10.

(4) Setup a Freestyle job (for ease; also happens on pipeline) that syncs a workspace containing the utf8+w file and publishes any changed files that is pinned to run on Windows 10 slave.

(5) Run the job. Reconcile will always detect the utf8+w  file as a file to publish. For example:

... p4 opened -Cjenkins-Windows10-Freestyle_c1-0 //jenkins-Windows10-Freestyle_c1-0/...
 +
... ... edit //depot/project1/test.ps1
... submitting files

(6) At the command line 'p4 reconcile -a -e -f' does not detect files as changed. For example:

C:\Users\karl\AppData\Local\Temp\workspace\Freestyle_c1>p4 -p C1_server:1667 -u super -c jenkins-Windows10-Freestyle_c1-0 reconcile -e -a -f //jenkins-Windows10-Freestyle_c1-0/...
//jenkins-Windows10-Freestyle_c1-0/... - no file(s) to reconcile.

Therefore suspect this is a P4Java bug.