I'm getting the same issue reported in message #5 with flex 2.6.1-1.3 amd64.
$ echo %% | flex ; gcc -c -Wsign-compare lex.yy.c
lex.yy.c: In function ‘yy_get_next_buffer’:
lex.yy.c:557:18: warning: comparison between signed and unsigned integer
expressions [-Wsign-compare]
for ( n = 0; n < max_size && \
^
lex.yy.c:960:3: note: in expansion of macro ‘YY_INPUT’
YY_INPUT( (&YY_CURRENT_BUFFER_LVALUE->yy_ch_buf[number_to_move]),
^~~~~~~~
Downgrading to 2.6.1-1.2 did not solve the issue.

