My suspicions go to the ungetc function :

This is how I instrumented it :

static unsigned int get_char()
{
	unsigned int c;
	c = fgetc(f_in);
	if (c == '\n')
		linenum++;

        printf("Got '%c'\n", c);

	return c;
}

static void unget_char(unsigned int c)
{
	ungetc(c, f_in);
	if (c == '\n')
		linenum--;

        printf("Ungot '%c'\n", c);
}

For the parsing of the ? phoneme this is what I get :

Compile phoneme: ?
Got '/'
Got '/'
Got ' '
Got 'g'
Got 'l'
Got 'o'
Got 't'
Got 't'
Got 'a'
Got 'l'
Got ' '
Got 's'
Got 't'
Got 'p'
Got '
'
Got ' '
Got ' '
Got 'v'
Got 'l'
Got 's'
Got ' '
Got 'g'
7: vls -> 'g'
Ungot 'g'
Got 'g'
Got 'l'
Got 't'
Got ' '
Got 's'
7: glt -> 's'
Ungot 's'
Got 's'
Got 't'
Got 'p'
Got '
'
Got ' '
Got ' '
Got 'l'
7: stp -> 'l'
Ungot 'l'
Got 'l'
Got 'e'
Got 'n'
Got 'g'
Got 't'
Got 'h'
Got 'm'
Got 'o'
Got 'd'
Got ' '
Got '3'
7: lengthmod -> '3'
Ungot '3'
Got '3'
Got ' '
Got ' '
Got ' '
Got '/'
3: 3 -> '/'
Ungot '/'
Got '/'
Got '/'
Got ' '
Got '?'
Got '?'
Got '
'
Got ' '
Got ' '
Got 'n'
Got 'o'
Got 'l'
Got 'i'
Got 'n'
Got 'k'
Got '
'
Got ' '
Got ' '
Got 'V'
7: nolink -> 'V'
Ungot 'V'
Got 'V'
Got 'o'
Got 'w'
Got 'e'
Got 'l'
Got 'i'
Got 'n'
Got ' '
Got ' '
Got 'g'
7: Vowelin -> 'g'
Ungot 'g'
Got 'g'
Got 'l'
Got 's'
Got 't'
Got 'o'
Got 'p'
Got '
'
Got ' '
Got ' '
Got 'V'
7: glstop -> 'V'
Ungot 'V'
Got 'V'
Got 'o'
Got 'w'
Got 'e'
Got 'l'
Got 'o'
Got 'u'
Got 't'
Got ' '
Got 'g'
7: Vowelout -> 'g'
Ungot 'g'
Got 'V'
Got 'o'
Got 'w'
Got 'e'
Got 'l'
Got 'o'
Got 'u'
Got 't'
Got ' '
Got 'g'
7: Vowelout -> 'g'
Ungot 'g'
Got 'g'
Got 'l'
Got 's'
Got 't'
Got 'o'
Got 'p'
Got '
'
Got ' '
Got ' '
Got 'W'
7: glstop -> 'W'
Ungot 'W'
Got 'W'
Got 'A'
Got 'V'
Got '('
7: WAV -> '('
Ungot '('
Got 'W'
Got 'A'
Got 'V'
Got '('
7: WAV -> '('
Ungot '('
Got '('
Got 'u'
Got 's'
Got 't'
Got 'o'
Got 'p'
Got '/'
Got 'n'
Got 'u'
Got 'l'
Got 'l'
Got ')'
2: ustop/null -> ')'
Ungot ' '
Got ' '
Got 'b'
Got 'r'
Got 'k'
Got '
'
Got ' '
Got ' '
Got 'F'
7: brk -> 'F'
Ungot 'F'
Got 'F'
Got 'M'
Got 'T'
Got '('
7: FMT -> '('
Ungot '('
Got '('
Got 'r'
Got '3'
Got '/'
Got 'r'
Got '_'
Got 't'
Got 'r'
Got 'i'
Got 'l'
Got 'l'
Got ')'
2: r3/r_trill -> ')'
Ungot ' '
Got ' '
Got ' '
Got ' '
Got ' '
Got 'E'
Got 'n'
Got 'd'
Got 'S'
Got 'w'
Got 'i'
Got 't'
Got 'c'
Got 'h'
Got '
'
Got '
'
Got ' '
Got ' '
Got ' '
Got ' '
Got 'V'
7: EndSwitch -> 'V'

We can clearly see that after vowelout and WAV we don't get what we have unget. Worse, there's a full jump after the ustop/null that sends us way beyond the current position.

What's your opinion on this ?

Edit: This might be a wrong guess, it looks like there is also the UngetItem functions which may interfere here. Still investigating.