How to capture traffic from multiple user accounts with Fiddler run as a service?

You haven't mentioned which operating system you're using. To get other user-accounts to trust the Fiddler root certificate, it must be installed in the machine certificate store, not the user store. By default, Fiddler will prompt you to do this on Windows 8 and later. 

From the Fiddler book:

1.        In Fiddler’s Tools > Fiddler Options > HTTPS tab, click Export Root Certificate to Desktop.

2.        Launch mmc.exe.

3.        Click File > Add/Remove Snap-In.

4.        Select the Certificates snap-in and press Add.

5.        When prompted This snap-in will always manage certificates for: choose Computer Account

6.        Click Local Computer, then Finish, then OK.

7.        Open the Certificates (Local Computer) node.

8.        Right-click the Trusted Root Certificate Authorities folder and choose All Tasks> Import.

9.        Choose the file you exported in step #1 and import it.

Regards,
Eric Lawrence
Telerik