A 'logger-head' was literally a 'block-head'. A logger was a thick block of timber which was fastened to a horse's leg to prevent it from running away. In the 17th century, a loggerhead was also recorded as 'an iron instrument with a long handle used for melting pitch and for heating liquids'. It is likely that the use of these tools as weapons was what was being referred to when rivals were first said to be 'at loggerheads'.
http://www.phrases.org.uk/meanings/at-loggerheads.html