its works when you set it manually to 1GBps on both ends ?
also stupid-looking/sounding guess about cable[but can be too, btw]:
cable degradation[but over NOTABLE time]quite usual/eventual, ie plastic-made insulator - relatively short-living thing.
check with different cable[new, shortest as possible. for test - buy STP Cat6A short cable[dubbed "patch-cord" in price-lists].
another stupid question:
did you put it into one of first five ports ? [not 100Mbps on second switch]
auto-negotiation on interface is turned-on, for sure ?
from page http://wiki.mikrotik.com/wiki/Manual:Interface/Ethernet
set to "yes" ?
same - about "full-duplex".[generally not need to set it otherwise]