The Treasury press release has more details than the State press release on what they believe the situation with the state of Iran is; note that it also implicates "Kuwait jihadist donors":

Al-Fadhli began working with al-Qa’ida’s Iran-based facilitation network in 2009 and was later arrested by the Iranians.  He was subsequently released by the Iranians in 2011 and went on to assume the leadership of the facilitation network from Yasin al-Suri later that year. 

In addition to providing funding for al-Qa’ida activities in Afghanistan and Pakistan, this network is working to move fighters and money through Turkey to support al-Qa’ida-affiliated elements in Syria.  Al-Fadhli also is leveraging his extensive network of Kuwaiti jihadist donors to send money to Syria via Turkey.

Treasury previously took action against this al-Qa’ida funding and support network in July 2011 when it designated Yasin al-Suri and five other al-Qa’ida members pursuant to E.O. 13224.  This network uses Iran as a critical transit point and operates under an agreement between al-Qa’ida and the Iranian government.  Under the terms of the agreement between al-Qa’ida and Iran, al-Qa’ida must refrain from conducting any operations within Iranian territory and recruiting operatives inside Iran while keeping Iranian authorities informed of their activities.  In return, the Government of Iran gave the Iran-based al-Qa’ida network freedom of operation and uninhibited ability to travel for extremists and their families.  Al-Qa’ida members who violate these terms run the risk of being detained by Iranian authorities.  Yasin al-Suri agreed to the terms of this agreement with Iran with the knowledge of now-deceased al-Qa’ida leader ‘Atiyah ‘Abd al Rahman.

While I agree it's important to be skeptical about what western governments say about Iran and about the quality of western governments' intelligence about Iran, I think it's also important to keep an open mind to theses possibilities as well:

that what is called "Al Qaeda," may have changed, and

that the very much changed situation in the neighborhood may have caused alliances to become different than they were in the Bush years. I think it's important not to read the news about the area as if what was true during the Bush years is always going to continue to be true. I.E., just because the Bush administration lied about Al Qaeda in Iraq and Iran does not mean that they or similar will never ever will operate there nor does it mean that state of Iran cannot change its mind about what they think is beneficial to their core strategic interests.

Seems to me that these US statements could demonize and implicate the state of Iran much more than they do if they wanted to, but they instead allow ambiguity by the use of the term "Iran-based."

I could be wrong but sense it is more of an attempt by the US to keep names that they consider major Al Qaeda out of the Syrian insurgency, and it may actually be targeted more towards Sunni-radical funding than towards Iran. Or at least to have on the record that they saw the problem developing and were against it, even though they are not screaming directly at the leaders of Gulf States about it right now. A "CYA" as it were.

In a roundabout way, this could also be an admission that the US government doesn't think the Iranian government is as all-controlling of everything that happens within its borders as more conservative anti-Iran western groups tend to believe.(And you, apparently?) I think more like this: if Iran is so much in control of what goes on within its borders, how come it has not been 100% successful at stopping attacks by Jundallah within its borders? We don't know for a fact that this is news that the west has, maybe through Turkey, for example, that Iran doesn't and that Iran , after checking it out itself, could say, arrest them for violating the terms of their agreement in the next week.

What I bascially think is that it's a wait and see, a "developing."

One thing I am certain of is from extensive reading at the time that  during the Bush years when several Al Qaeda of import were being held by Iran, that the story ended up being one of Iran simply holding them as possible pawns. They weren't sure of what to do with them, didn't want them going and causing more havoc in Afghanistan, and so basically thought, what the heck, as long as we make sure and keep them under tether, they might use them somehow in the future.