So I've hit two problems in my game.
If a system is protected by a passkey system, there is apparently no difference in the difficulty in accessing the node, but the next time the access log is updated, the hacker is detected and an active alert is issued. This can be avoided by hacking the access log. So, my question is, "When does the access log get updated?" Also, if the solution is to edit the access log, which most hackers are going to do most of the time anyway, why bother with the expense?

<edit> I found the access log update. A number of combat turns equal to the System attribute of the node. </edit>

Linked passcodes, on the other hand, seem to have very little info available. If a system uses a linked passcode, and I do not have the link, what effect does it have on my hacking?

On a related note, does Jazz give matrix users an extra initiative pass? It seemed wrong, but I couldn't find anything in the book to back me up.

Regarding Jazz in AR yes it does, in VR no it doesn't.

I agree, but is there a reference? I was argued with and couldn't back it up

It's simple really, Jazz affects the meat body and the meat has no effect on how fast you are in the Matrix in VR. Does wired reflexes work in VR? No. Move by Wire? No. Increase Initiative spell? No. Pg 226 of SR4A shows how to calculate your matrix VR initiative while Unwired provides another way to increase your passes and Augmentation has the Simsense Booster cyberware for another pass in the matrix in VR. Those are the only way to increase VR passes outside being a technomancer. The drugs only affect the meat.

I cannot find a direct quote that says that passes aren't carried over in matrix initiative, however it clearly outlines that
a) Matrix initiative is seperate from physical initiative and don't run off your attributes (p. 226, 236 SR4A)
B) You are cut off from your physical body relying on the machine to decode the information (p.226)

OK, good enough for me. I'll just say NO and not argue about it Thanks.

Now, what about the linked passcode?

Sorry for being a bit late. My understanding based on the SR4A book (p 225) is that it would affect probing more than hacking on the fly, since it's just one more way of verifying that a user is allowed to use a given account/access ID. The RAW states that trying to log into the system without the passcode will result in the login attempt being denied, so I would guess that the hacker would need to create themselves a fake passcode on top of their fake account. How exactly that hashes out into mechanics, I don't know - maybe a higher threshold for probing tests? (This is mostly speculation on my part - if someone has a definite answer, I'd be curious to see it.)

Not sure if OP has already found an answer for this, after some cobbled-together research I think the passkey and passcode actually function the same way: if you're in the system and the access log realises you don't have it, you're booted. Logic seems to suggest there's a separate "user has valid passcode" flag, in the same way that there would be a "user has valid passkey" flag for the passkey version, and editing the system log fakes those flags for you.