There was a known issue where the download time was 4 times slower on CW ColdFire version 6.3 and 6.4 than on the 6.2 version using P&E MicroUSB. Actually this was not a bug; the root cause was as follows: CW 6.2 doesn't take the access size from .mem file into account and is using 4 bytes access by default. CW 6.4, on the other hand, is using the access size information from mem file and it is 1 byte by default. As a workaround please set the memory access size to 4 in the appropriate mem file in order to achieve the same speed as in the CW 6.2. You can set the .mem file in your project settings CF Debugger Settings panel->Use Memory Configuration File, after editing this file with memory access size to 4 bytes, like in the following example:
// Memory Map:
range 0x00000000 0x03FFFFFF 4 ReadWrite // 64MB DDR SDRAM
range 0x20000000 0x20000FFF 4 ReadWrite // 4K SRAM0 (RAMBAR0)
range 0x20001000 0x20001FFF 4 ReadWrite // 4K SRAM1 (RAMBAR1)