Hi,
I just checked on my Linux system.
SAPLogon entry is "conn=/H/rz3.mycompany.com/S/3299/H/10.2.2.117/S/3280"
When I create a new ABAP-project the entries are imported correctly:
Application Server 10.2.2.117
Instance number 80
Router-String: /H/rz3.mycompany.com/S/3299
I use SAPGui 7.40 and Eclipse Luna
Maybe this helps.
Good luck!