Any specific reason to write the or statement as two separate if clauses?

I believe in other parts we do it ((true & x & y & z) | (false & a & b &c )) - as multiline checks;

I don't like them both get executed "always", so at the very least, an "else" just before the 2nd if would be good.

The logic looks ok to me.

I agree with Richard, better one complex if clause. The two clauses are mutually exclusive as one wants TOF_TS and other !TOF_TS, so cc_cong_signal() can be executed only once. My first reading was that it is intentionally written this way cause we may want two calls into cc_cong_singal(), so it was a misleading reading.

Oh, the upper level embracing if can also be merged into one big clause:

if ((tp->t_rxtshift == 1 &&
    tp->t_flags & TF_PREVVALID &&
    tp->t_badrxtwin != 0) &&
    (((to.to_flags & TOF_TS) != 0 &&
    (to.to_tsecr != 0) &&
    TSTMP_LT(to.to_tsecr, tp->t_badrxtwin)) ||
    ((to.to_flags & TOF_TS) == 0 &&
    TSTMP_LT(ticks, tp->t_badrxtwin))))
        cc_cong_signal(tp, th, CC_RTO_ERR);

This will also fix lines longer than 79 chars. IMHO, we may slightly violate style(9) and add single space indentation to highlight our three main large blocks (a && (b || c)).

It was a try to break things up for improved readability by humans.

Now using one and two spaces of indentation to make the expression more readable.