You're not being very clear: you state what the law/Constitution requires, but don't state what you think the violations are - perhaps by stating the criteria you mean to imply all criteria were violated? Let me make it clear - there are two separate issues:
1. Was Padilla eligible for long-term detention based on the Constitutional criteria for suspending the writ of habeas corpus?
2. Was the President authorized to make that call based on Congress's war authorization?
I'm guessing that your post is meant to imply you think the answer to both questions is "no".
In the courts, the answer to #2 was what went back and forth, with the last decision being a "no" answer. Your first link says in the first sentence on page 4 that because the answer to #2 was "no", they declined to addresses question #1. Despite being more important and broader, it is putting the cart before the horse: you have to have the right signature on the paperwork before you decide if the content of the paperwork is correct.
Your second link answers "yes" to #2 and therefore addresses #1: It states explicitly that Padilla "clearly and unmistakably" qualifies for detention under the Constitutional criteria. How could it be otherwise? Fighting a war against the US government on American soil is absolutely an invasion or rebellion (with the difference between the two simply being the motivation).
Again, it is my opinion that by the criteria of the Constitution, Padilla's detention was legal. This is physical justice (as explained in my discussions of the multiple definitions of "justice"). The answer to #2 is debateable and I don't have a firm yea or nea opinion on it, but only comment that when the (potential) violation is almost literally a matter of who'se signature is on the piece of paper authorizing the detention, it is an injustice of paperwork and not an injustice of action. And I care much more about action than paperwork.
I may need to make another thread for this point, but a recent counter-example in Philly has me pretty annoyed: 30 years ago we had a guy essentially execute a cop and he'd been on death row until a few days ago. An appeals court ordered a new sentencing hearing due to the potential that the jury had been confused by their orders on sentencing. You see, mitigating circumstances don't require a unanamous vote, but aggravating circumstances do and the way their orders were worded, it was potentially confusing (though no evidence of confusion existed and interviews with the foreman recently show there was no confusion). So for a weak wording of procedure that was moot anyway, justice is not going to be carried out: after 30 years of appeals, the DA is no longer going to pursuse it. More often it seems, it is the paperwork justice that prevents physical justice from being carried out. And that annoys me.