When Rebbi Meir teaches in the Mishnah that the person's Eruv is a Safek Eruv, Rashi explains that the reason for this is because we are not sure where the person wanted his Shevisah to be: at home, or 2000 Amos away.
This is an interesting Chidush. Why should his Eruv be a Safek because we do not know his intent? He knows whether or not he wanted his Shevisah to be in his house! If he wanted his Shevisah to be at home, let it be at home -- what difference does it make if we do not know his intention!
That's a good question. The obvious answer would seem to be that "Devarim she'b'Lev Einam Devarim." However, if so the Eruv certainly would not be an Eruv (and it would not be a Safek Eruv) since there were no spoken "Devarim" to make it into an Eruv. In addition, the Rashba (Kidushin 50a) teaches that Devarim sheb'Lev are always Devarim if they are not contradicted by a person's words, and here there were no words to contradict his thoughts.
Perhaps Rashi means that we are in doubt as to what the "Umdena" (the person's assumed intention) is in this case: Is there an Umdena that he wants to make the Eruv at home, or is there an Umdena that he wants to make it 2000 Amos away? Since there may be an Umdena that the Eruv is 2000 Amos away, it takes effect mi'sSafek. In addition, if there is an Umdena (based on the person's actions) that he does not want the Eruv to be 2000 Amos away, even if in his mind he decided otherwise, his actions would be contradicting his thoughts and his thoughts would be Devarim sheb'Lev. Although it sounds strange to propose a "Safek" about whether there is an "Umdena" (the two seem to be mutually exclusive, as the KETZOS HA'CHOSHEN writes in CM 250:5), nevertheless we find precedents for such situations, as the Acharonim discuss.
Alternatively, the Mishnah may be referring to a case in which the person forgot what he had intended, and that is why he is deemed a Safek.