i have timing issues too. only way i can get them right is listen to the song i'm practicing enough so that the song is stuck in my head so i kinda like hear it in my head before i play it?
i dont really get playing with a metronome, cant seem to get it right and makes me think too much

as in i can't divide the beats and stuff like that i think :S

i cant play a song with the metronome on, confuses me because i think about it too much =/
but when practicing runs i play with the metronome of course

kinda like the problem i have. irregular time signatures or stuff like that

i just learned some jazz timings today and its screwing with my brain

i do like what echo does, listen to the song enough and play it from your head counting spoils the fun of playing

ah i think i have what you mentioned^
the building the metronome in my mind. now everytime i hear a song somewhere(At a restaurant etc) i'll start tapping my foot to match the beat