If you work with the Machines, you don't get attacked if you've hacked the nodes... if you work for Zion, however, you will get attacked even if you do have the nodes hacked. The only difference is you'll be attacked by lower level Agents (100 as opposed to 255) that can be killed with a concerted team effort.
This change is because the Truce has fallen and the Machines and Zion are once again at war. It is, however, a contentious change seeing as how there really isn't a similar "penalty" to balance things on the Machinist side... it fits well with the story but, as you have noticed, can have a detrimental effect on the gameplay side of things.
.. of course, if you are working with the Machines and this is still happening then I guess you're just really unlucky. hehe
As above with a few additions...
lvl255 agents will always be "named", such as Agent Brown, or Agent Jones.
lvl100 agents will just say Agent
and yes, the key here is that you can just HJ straight up, and a lvl100 agent will dissapear, tho they will continue to reappear periodically as long as you are in any District other than Richland.
The thing i dont get is.... why don't they spawn for Merv's? There has never been a Truce between the Machines and Merovingian, so why don't their operatives spawn lvl100's? Or do they and i just don't know it? In fact, it seems like they should have all along, realistically. Anyway, there I go again looking for logic in the workings of this game....
the good news is that if you hyperjump (even straight up) the agents lose interest and disappear. so unless you are in IL in battle you can escape them VERY easily.
T
They should attack Mervs now as in one of the last updates it was made so agents are now machine aligned. Meaning that if you arent machine you might get jumped.
Side Note:
Agents do get annoying but just always keep HJ loaded and you should be ok. And watch your agent meter and messages. They alert you when a agent is closing in on ya.
Another quick addition I found about the "Agent" v.s. Agent *Name*When the Agents with names come after you you will always have about 2 seconds to see a civilian spawn until they attack you.
The lvl 100 Agents do not spawn indoors, whilst the Node Agents do if you haven't tagged the appropriate node. So indoors while on a mission you are safe unless you havent tagged the area's node, ha or unless you spend too long in the mission area!
You'll find that in LE's when indoors those who get killed by Agents are those that haven't been bothered in tagging the nodes (or are not at a high enough level to get the access key)