This problem has been corrected in RSA ClearTrust 5.5.3; the log files now correctly rotate according the to file size in kilobytes.
Also, you can modify the cleartrust.lserver.log.size value accordingly when applying RSA ClearTrust 5.5.3.x or later patch. For more information, see the related solution
Log rotation of the lserver.log file in RSA ClearTrust does not seem to work.
# The log file size (in kilobytes) for a Log Server log file. When the
# log file reaches this size, it is rotated -- that is, the log file is closed,
# renamed by appending a sequential number, and a new log file is started.
#
# Allowed Values:
# A positive integer.
#
# Dependencies:
# None
#
# Default Value:
# 1000
#
cleartrust.lserver.log.size=1000