I have some questions:
1. Is it possible that a single port from a IP to cause this?
To understand why fragmentation may be occurring and why it may also be causing your problems, you would need to know the details of how IP fragmentation occurs as well as understanding the differences between TCP and UDP.
In a nutshell (this is very simplistic), a large network such as the Internet is divided into segments, each segment is connected to another segment via a router. Each segment typically has a set size that it will allow for datagrams that travel over that segment. This is called the MTU (Maximum Transmission Unit). If a datagram is larger than a specified MTU it will be fragmented.
When a datagram is fragmented, each piece is given a new header and sent on its way. The path one individual piece takes may not be the same as any other piece. When the pieces arrive at their destination they are reassembled. However if one piece is missing the datagram is discarded.
With TCP this is less of a problem because TCP has the ability to ensure retransmission of any lot pieces. Typically, UDP does not.
So, In your scenario, for whatever reason, it seems that the connection to one particular server is less reliable than others. It may be a fragmentation issue, resulting in lost datagrams or it may be some configuration issue with that particular server.
2. Why does comodo doesn't show blocked entries?
It will only show log entries for rules for which logging has been enabled, either allow or block.
3. Since we can connect to the server by unchecking that box, is there a program to fully check/see the detials while connecting to the server?
There are some things that can be done to investigate, obviously talking to the server host to determine their configuration parameters may enlighten us further.
Failing that, you could analyse the traffic leaving your client using something like
Wireshark You could also try to investigate the maximum MTU size by using ping with different ICMP sizes.
ping -f -l 1472 (insert the server details here)
Keep reducing the number until you no longer receive fragmentation required messages. Once you have this value you can change the MTU size on your PC.
Seems like a lot of aggravation to me...