Most likely, there is an issue with your device driver. Perhaps Xon/Xoff flow control does not get enabled properly on a lower level while CoolTerm thinks that it is. I would recommend installing the latest driver. Which Arduino model are you using?
I'm not aware of any other drivers for the Arduino Uno. Do you have access to an Arduino that uses an FTDI chip instead of the ATMega16U2?
You might also want to try this with a different terminal, just to rule out that there is some weird interaction between the driver and the API CoolTerm is using that causes this problem.
Meanwhile, can you send me your sketch, or a test project that demonstrates the issue? I can get my hands on an Arduino Uno R3 to see if I can replicate this. Please send it to my e-mail address (you can find it on my website http://freeware.the-meiers.org/)
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