But not necessarily at all frequencies. 1000Hz is a pretty high note, its not surprising it wouldn't clip there, it's more likely to clip at lower frequencies which require more power. Also since it only needs to play 1 frequency, its got a lot more resistance to clipping.
That doesn't necessarily mean that your tuning didn't keep it out of clipping range though. Your EQ settings may be good and keep it out of clipping, a good tune should keep it out of clipping. Also audio sources tend to be of very different volume levels, with some songs being recorded at +12dB, some at 0db, etc. (all in relation to another). The test tone might be recorded at a lower volume than music, so while it doesn't clip on the tone, it would clip on music.