Does Jan's ability work with Protons etc???

Yes.

Ok cheers....Where is the justification for this? I ask as this came up in a tournie and the opponent said that Sec weapons can not be adjusted.

Jan's ability is not limited to primary weapons. Her card has no such limit. Nor is there any such limit anywhere in the rules.

"... Sec weapons cannot be adjusted" would need to be proven. Which it cannot. Nowhere in the rules is anything like that.

Note: Howlrunner is limited to primary weapons. The opponent was probably confused by that.

Edit:

Secondary weapons are not adjusted by range or by shooting through obstacles. Jan's ability is neither of that.

Depending on the range between the ships, the attacker or defender may roll additional dice during this attack (see “Roll Attack Dice” and “Roll Defense Dice” on pages 11–12). Range bonuses only occur when a ship is attacking with its primary weapon

As per the FAQ When measuring range during combat, if the edge of the range ruler between the closest points of the two ships overlaps an obstacle token, the attack is considered obstructed.

If an attack is obstructed the defender gets to roll an additional defense dice.

If your using Jan ors you get to use additional dice.

Wedge + APT it is then....Thanks guys.

Apt and wedge is a great combo only problem is he is usually the first one you shoot at.

If an attack is obstructed the defender gets to roll an additional defense dice.

That includes secondary weapons. I got that wrong in my previous post.

It's pretty simple. If the ability references primary (Howlrunner) or secondary (Krassis Trellix), that's what it affects.

If it doesn't specify one or the other (Jan, Horton, etc) it works for either.