The Mishna does not permit the Hatmonah of a food which is being insulated for the first time on Shabbos but does permit Hatmonah of that which was already insulated from Erev Shabbos and was since removed. The reason for this distinction, as is given by the commentaries, is that we assume that latter to be much warmer than the former and therefore there is no fear of him coming to reheat a cold food. If this is so, why don't Chazal merely permit the insulation of a food which is now warm (or hot) and prohibit the insulation of a food which is not warm (or hot). Why should it depend upon whether or not it was insulated Bain Hashmoshos?
Dov Lew
Very good question. It seems that generally, food will not be hot on Shabbos unless it was insulated before Shabbos. Otherwise, it will lose its heat between the time that it is removed from the fire and the time that Shabbos enters. Therefore, the Rabanan prohibited insulating anything that had not been insulated prior to Shabbos. Even though at the moment that Shabbos enters the food is hot without being insulated, nevertheless it is prohibited to insulate it, lest one think that it is permitted to insulate cold food (that is, when this pot of food loses its heat in a matter of minutes).
According to the RAMBAM (see Inisghts to Daf 34a), who holds that the Rabanan prohibited Hatmanah in material that does not add heat lest one do Hatmanah in ashes, it certainly makes sense that all Hatmanah, from the beginning of Shabbos, is forbidden for this reason.