The parsha begins, “Eleh pekudei hamishkan, mishkan haedus asher pukad al pi Moshe…”. The Medrash refers this pasuk to the pasuk in Mishlei (28:20) “Ish emunos rav brachos”. The Sfas Emes explains that the Ish emunos is Moshe Rabbeinu and what the Medrash is telling us is that although counting something is not a siman brocha when the counting is done by an Ish emunos then brocha will be bestowed on the counted subjects.
The Kli Yakar in the beginning of parshas ki sisa explains the idea behind why one should not count and why counting brings ayin raah. When one counts something he is in essence giving this object its own individual importance, thereby creating additional awareness of it in shamayim. This awakens the debate as to the rights of the object, and all the relevant zechuyos and chovos are judged.
The Sfas Emes this week expounds this idea and with it beautifully explains the Medrash. All the good bestowed upon this world comes from a single higher source and as you distance from the source the good is diminished. From this shoresh hayachid hashmeymi branches out big then smaller and smaller branches, and the smallest furthest branch profits the least from the goodness supplied by those roots. When somebody counts something the individuality and importance that he applies to it separates it further from the source as it now has its own new identity. It is a new branch of its own. Before it was counted it was a part of the bigger branch, closer to the roots. This is why counting usually brings less brocha.
In many places the Sfas Emes explains that the root of the word emunah means connecting the subject back to its real true source. With this the medrash becomes beautifully clear. The medrash is explaining the pasuk as follows. Why does the pasuk mention that the counting was done by Moshe? The Torah wants to teach us that although it was counted which would normally bring about a lack of brocha, when it is counted by Moshe Rabbeinu an ish emunos a man of true emuna whose whole being was to bring everything back to the mekor hatov, then the counting does not distance it from the source. On the contrary writes the Sfas Emes the counting brings it closer to brocha. When Moshe rabbeinu counted, unlike a regular person, instead of accounting importance to each object he accounted the importance to everything as a whole single unit, not as many individuals. Thereby connecting everything back closer to the single roots of tov from where it stems.