Hi,
As I understand, when the server sees the SYN packet the TCP MSS should have been adjusted to 1350 by SRX1, however the server may not reply with an MSS of 1350. The payload could be higher depending on its MTU:
This Maximum Segment Size (MSS) announcement (often mistakenly called a negotiation) is sent from the data receiver to the data sender and says "I can accept TCP segments up to size X". The size (X) may be larger or smaller than the default. The MSS can be used completely independently in each direction of data flow. The result may be quite different maximum sizes in the two directions.
Devices may wish to use a larger MSS if they know for a fact that the MTUs of the networks the segments will pass over are larger than the IP minimum of 576. This is most commonly the case when large amounts of data are sent on a local network; PMTUD is used to determine the appropriate MSS.
http://www.tcpipguide.com/free/t_TCPSlidingWindowDataTransferandAcknowledgementMech.htm
I understand when a large IPSec packet is received by SRX1 it will send ICMP destination unreachable Fragmentation needed and DF set [ICMP Type 3 Code 4]. If icmp is filtered on the other end of the tunnel, PMTUD is not possible and the packet size will not be adjusted.
Maybe you could check this on SRX2 if you see any ICMP Type 3 Code 4.
Cheers,
Ashvin