There are two separate issues at hand with regard to Geneivah that might be confusing you. The first is Geneivah as opposed to Gezeilah. This issue only pertains to paying double (for Geneivah or Toen Ta'anas Geneivah, as opposed to Gezeilah). The other issue is Geneivah (or Gezeilah) as opposed to Ones. This issue pertains to the laws of Shomrim; a Shomer Sachar or Socher is only responsible to reimburse the owner for Geneivah and not for Ones.

Rav Zeira explains that the Shomer originally claimed Listim Mezuyan took the object from him, thereby exempting himself for responsibility for the theft (i.e. the second issue stated above), since Listim Mezuyan is certainly an Ones no matter whether it is considered Geneivah or Gezeilah with regard to the first issue.

The Shomer, however, decided to volunteer to pay the owner for the object anyhow (just to show what a good friend he is). Afterwards, the object was found, and the thief turned out to be not an armed robber (Listim Mezuyan), but a normal sneak-into-the-house-in-middle-of-the-night Ganav. Listim Mezuyan is considered Gezeilah, and exempt from paying double, but a regular Ganav does pay double. Since the thief was indeed a regular Ganav, he must pay double, and the Shomer takes the double payment since he already paid for the object. That is the answer to your question.

Just to clear the air, there may have been other points that added to your confusion which I shall address in brief:

1. If the Shomer himself claimed that the robber was armed (and that he therefore would not have to pay double, if caught), how can we later "prove" that the robber was not armed but was a midnight thief? Even if we bring testimony to that effect, the Hoda'as Ba'al Din of the Shomer should override the testimony and deprive him of the double payment! (Or Same'ach, She'eilah 8:1)

2. The Gemara teaches that a Shomer takes the double payment even if he did not pay (or, to be exact, offer to pay) the owner "out of the goodness of his heart." Rather, even if he is judged to be responsible for the object he is watching, from the moment he agrees to pay what he is due to pay, the Shomer gets the Kefel if the Ganav is found (Bava Metzia 34a). If so, why did the Beraisa go out of its way to choose a case where the Shomer volunteered to pay out of his good will? Even if the Shomer claimed that a normal Ganav took the object, he would also take the double payment!

3. The Gemara in Bava Metzia 34a cites this very Beraisa. But Rashi there explains that the Shomer indeed did claim that it was stolen by a normal thief (and not an armed robber), and that he receives the double payment because he was "a nice guy" and didn't try to weasel out of paying by claiming (falsely) that an Ones happened to the object. This seems to contradict our Gemara, which learns from the words of the Beraisa that the Shomer made a claim which should have exempted himself from payment, had he not volunteered to pay! (RASHASH and CHIDUSHEI RABEINU MEIR SIMCHA in Bava Metzia).

It seems to me that the answer to these questions (at least according to Rashi) is as follows. Rashi did not learn the answer of Rav Zeira as we explained it above (which is also the way almost everybody who learns the Gemara explains it). Instead, he learned that Rav Zeira's answer is that in the case in the Beraisa witnesses testified that they saw the object stolen from the Shomer, but they could not say what kind of crook took the object (i.e. Mezuyan or not). The Shomer admits that the thief was a normal crook (Ganav) and not Listim Mezuyan. When the Gemara says "b"Toen Ta'anas Listim Mezuyan," it does not mean that the Shomer actually claimed Listim Mezuyan. It means that the Shomer could have exempted himself by claiming that it was taken by Listim Mezuyan, and that is why the Beraisa says "Eini Nishba" (i.e. he could have sworn and exempted himself). The Shomer receives the double payment in such a case, exactly as Rashi explains in Bava Metzia.

I hope this helps you. Best wishes for a Chag Same'ach,

Mordecai Kornfeld