Carlos,
For us the issue was connected to many, many, GUI sessions not being released from the gateways after logoff. This was causing an issue where the communication was timing out waiting for an available session.
In our case, using tcode SM04 on each ECC application server, we could see extremely old non-active RFC sessions. After removing those session that were inactive for at least 24hrs (painstakingly, one-by-one) we saw immediate relief and the new RFC's stopped failing.
I'm pretty sure it's a kernel issue, but we only saw it in production where the load is great enough for it to surface.
Not really a resolution, but I hope that helps you find yours.
Jim
PS: You can easily see if this is part of your symptom by using tcode SM51 ==> Goto ==> User (click)
then Goto ==> System Wide List
and sort the output by "dialog time"
(My references are on ECC 7.40 EHP7)