Sounds like your Virtual Serial Port driver is getting stuck on some timeouts or buffers. The IDE calls avrdude with a specific protocol to match with what is built into the Arduino's bootloader, loaded on the AVR. There are other bootloader (in fact many, too many to mention), some of which may have different timing and such, but to use them would basically no longer be Arduino. to see the possibilities .\avrdude.exe -c.
If you are just trying to get a dump of what is going over the Serial port. I have used Virtual Serial Ports Emulator . It is very versatile in that its modular, allowing you to build up what you want.
Also, as mentioned from the other threads about this, note the data over the serial port is formated ontop of the STK500 protocol. You also mention in other thread that you don't want to use another tool to get the data. Whereas in order to use another protocol you would need to change the source compiler.java and rebuild the project as to call avrdude with the new protocol. So you might as well just get it with another tool. see below this will tie back in.
you can get the raw binary, from what is being fed to avrdude. Where as it may not be initially obvious. As avrdude get ELF not BIN. The Arduino IDE contains all of avr-gcc and its tools. Where avr-objcopy located in .\Arduino\hardware\tools\avr\bin can convert the IDE's output that is funneled into avrdude, to the binary you likely desire. No need for scoping the serial port stream.
To do this by hand, You need to locate IDE's temp working directory, by enabling the IDE's verbose compile prints. And also likely put avr-objcopy in your path. then simply call it as in the below example, substituting your sketch's filename, in place of mine.
C:\Users\mflaga\AppData\Local\Temp\build6135656488044319492.tmp>avr-objcopy -I ihex FilePlayer.cpp.hex -O binary FilePlayer.cpp.bin
Where as you could replace avrdude.exe with a batchfile that calls both avrdude and avr-objcopy to automat
