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Connecting Ethernet Switch to System on Module

Hey at all,

we designed a new prototype. On this prototype we use an ethernet switch IC (from Microchip) with five integrated ports. 2 ports are not used, 2 of the other 3 are going of board and the last port connected directly to an ethernet module via MDI (4 signal pairs). There are no external components between switch and ethernet module. The ports which are going of board are typical connected via RJ45 and magnetics.

The problem we have is that auto negotiation  between switch and ethernet module varies in time. Sometimes it needs 10 seconds to get a link up and sometimes several minutes. But when the link up is done the connection is very stable and speed up to 1000 BASE-T works fine. 

So this is the connection which makes problems: PC -> cable -> RJ45 -> magnetics  -> (to port 3) switch -> ethernet module (port 1 of the switch)

When we connect the ethernet module with an external breakout board so we have following connection: PC -> RJ45 -> magnetics -> (to port 3) switch -> (from port 4) magnetics -> RJ45 -> cable -> ethernet module on  breakout board

The problem don't accure and the link up is ready after a short boot time. 

I have found in the internet different statements. Some say that there are no external components are needed. Some say that there is a need vor capacitors in series for the 8 signals (between switch and ethernet module) and some say that there is also a need for magnetics. But all of these statesments are from resources I do not trust 100% (for example reddit).

So maybe one of you have experience with this kind of problem and can help me with that. Is there a need for capacitors in series or should I place magnetics in between. Or is the problem something totally different.

Kind regards,

Jens