This is a lot of information, I will read it carefuly tomorrow, thanks a lot.
In, the meantime, I noticed a strange thing (I will also post my code tomorrow):

My routine reads 16 bits signal (PWM at 40KHz and TSOP4840 sensor-demod) through IR link using pulsin (each bit is 600Us either HIGH or LOW followed by a spacer of 600us LOW). The 16 bits are announced by a 2400 us HIGH followed by 600 us low. This header is ignored by the routine that waits for the header to end. The total length of the IR signal is (should be) about 22ms but when timing the routine that reads the signal, it takes (visualy, with a led) about 1 second!!! It is probably related to all the stuff we are talking about in the posts above.