You can determine if this is a problem if VPOP3 does not send autoresponse messages to incoming messages, but does to internal messages, and if you go to the Autoresponder settings in VPOP3 and click on 'View Log'
the resulting log shows the senders as being email addresses like SRS0=..... rather than the actual senders of the incoming messages.
(NB - the log only shows messages received within the "Don't send to same sender within x hours" setting for the autoresponder, so make sure that setting is not zero)
If the Sender email addresses have this format, then it means that your ISP's mail server is incorrectly performing 'Sender Rewriting Scheme' processing on the incoming message's SMTP return path.
SRS is a system designed for the situation where messages are to be forwarded on to another email address, so that bounces will go to the forwarding domain rather than the original sender and the forwarding domain can process them appropriately. However, SRS should only be performed by the 'authoritative' mail server for the domain, otherwise bounce messages or automatic responses will simply be undeliverable because the authoritative mail server will not understand the email address to send them to.
In this case, the authoritative server is VPOP3, not your ISP, so your ISP should not be performing SRS processing.
The ideal solution is if you can disable SRS on your ISP's mail server, so that the message's return path is left unchanged.
If that is not possible, then you can tell VPOP3 not to conform to the guidelines for automated responses (RFC 3834). The guidelines say that automated responses should always be sent to the Return Path (or SMTP "MAIL FROM" path) of the incoming message, which is what VPOP3 usually does
Workaround
In cases where this is not possible, because the ISP performs SRS rewriting and that SRS rewriting cannot be disabled, you can tell VPOP3 not to follow the guidelines and instead send automated responses to the 'Reply-To' or 'From' email address.
To do this, in the VPOP3 settings, go to Settings -> Autoresponder Settings, and clear the "Make autoresponders conform to RFC 3834" box, and then press the Submit button.
Now, VPOP3 will send autoresponses to the incoming messages's From or Reply-To email address.
Note that in this case, there is more likelihood of autoresponder loops (where two autoresponders send messages to each other for ever) so it is strongly recommended to use the "Don't send to same sender within x hours" setting in autoresponders to limit the number of autoresponse messages sent by VPOP3.