SES Light on again... Now what can it be? *UPDATED 07-23-07*

[Vonbimmer]

Well I had the SES light come on about two weeks ago with the following codes:
P1341 - Multiple cylinder misfire with fuel cut-off
P1351 - Misfire cylinder 5 with fuel cut-off
P1353 - Misfire cylinder 6 with fuel cut-off
P1349 - Misfire cylinder 4 with fuel cut-off
P1354 - Misfire during start cylinder 7
P1345 - Misfire cylinder 2 with fuel cut-off

My shop did a smoke test and diagnosed as leaking intake gaskets and valve cover gaskets, while they were there they did the valley pan.

The morning immediately after the repair I got the SES light back with:
P1354 - Misfire during start cylinder 7

The shop cleared this and said it could be a clogged injector or fuel pressure situation due to old filter / failing pump.

Now two weeks and 700 miles later the light is back on and I have the following codes:
P1341 - Multiple cylinder misfire with fuel cut-off
P1347 - Misfire cylinder 3 with fuel cut-off
P1345 - Misfire cylinder 2 with fuel cut-off

What else could be causing this? Is there a software update that I need to make it less sensitive?

* This did occur just after getting gas at Costco. Could it be bad gas?
** Note the X runs great and gives no indication of any of these issues.