[quote user="phoenixart"]

As far I know to classify a message as spam should be pretty easy. Right-click, then Spamhalter classification, and train message as spam (or click on the semaphore icon in the preview pane message)

Said that, I assumed that now Pegasus would move the message in the junk or suspicious mail folder. I've also turned on the Basic Spam Detection.

 [/quote]

No, it will not move that message anymore, it will use the now stored information to classify new incomming mail as spam. If you mover the message in the spamfolder yourself (any message) it'will be used to train spamhalter exactly the same as using the rightmouse.

 [quote user="phoenixart"]

The funny side of the story is that I'm finding non-spamming email in the junk folder, while the spam is still in New Mail folder.

Where am I wrong?

[/quote]

Training. Just move the message out of the spamfolder and Spamhalter will be trained that it's no spam.

As far I know to classify a message as spam should be pretty easy. Right-click, then Spamhalter classification, and train message as spam (or click on the semaphore icon in the preview pane message)

Said that, I assumed that now Pegasus would move the message in the junk or suspicious mail folder. I've also turned on the Basic Spam Detection.

The funny side of the story is that I'm finding non-spamming email in the junk folder, while the spam is still in New Mail folder.

Where am I wrong?

I am not sure if this is your problem but it does take some time to train a spam filter.  As well as using some spam messages to train as spam you need to chooses a range of not spam messages to train as not Spam.

 After the initial training keep retraining on all the mistakes.

It may help to have  Train on classification errors only turned on to start with and then set train always once the filter is right most of the time.

 It is worth being quite liberal about spam and allowing some advertising which may be unwelcome but is at least related to what you are doing through.