diff --git a/src/py/bbctrl/AuxPreprocessor.py b/src/py/bbctrl/AuxPreprocessor.py
index c4084be..13318a1 100644
--- a/src/py/bbctrl/AuxPreprocessor.py
+++ b/src/py/bbctrl/AuxPreprocessor.py
@@ -46,8 +46,42 @@ import tempfile
 
 
 # Strip line comments so we don't get fooled by "(M100 not really)".
+# Note this is a simple regex and doesn't handle nested parentheses
+# - which actually occur in real macro headers like
+# `(Composed from atoms: M102 = RELEASE (V1 on), M103 = CLAMP)`.
+# Use _strip_comments() below for a parser that does handle them.
 _PAREN_COMMENT_RE = re.compile(r'\([^)]*\)')
 
+
+def _strip_comments(line):
+    """Return `line` with paren comments and the trailing semicolon
+    comment removed. Handles arbitrarily nested parentheses (RS274
+    technically forbids them but real-world gcode comments often
+    contain prose with parens, e.g. `(M102 = RELEASE (V1 on))`).
+
+    Returns just the executable code, with the original whitespace
+    preserved between tokens."""
+    out = []
+    depth = 0
+    i = 0
+    n = len(line)
+    while i < n:
+        c = line[i]
+        if c == ';' and depth == 0:
+            break
+        if c == '(':
+            depth += 1
+            i += 1
+            continue
+        if c == ')':
+            if depth > 0: depth -= 1
+            i += 1
+            continue
+        if depth == 0:
+            out.append(c)
+        i += 1
+    return ''.join(out)
+
 # ATC pneumatics M-codes mapped onto hook events. M101 is
 # deliberately unassigned (see header).
 _ATC_M_CODES = {
@@ -135,8 +169,7 @@ class AuxPreprocessor(object):
         try:
             with open(path, 'r', encoding='utf-8', errors='replace') as f:
                 for line in f:
-                    code = _PAREN_COMMENT_RE.sub('', line)
-                    code = code.split(';', 1)[0]
+                    code = _strip_comments(line)
                     if _ATC_M_RE.search(code):
                         return True
                     if couple_active:
@@ -327,8 +360,7 @@ class AuxPreprocessor(object):
                 line = raw.rstrip('\n')
 
                 # Comment-only or blank lines pass through verbatim.
-                code = _PAREN_COMMENT_RE.sub('', line)
-                code = code.split(';', 1)[0]
+                code = _strip_comments(line)
                 if not code.strip():
                     fout.write(raw)
                     continue
@@ -347,10 +379,14 @@ class AuxPreprocessor(object):
                 if self._maybe_inject_a_down(code, fout):
                     rewrote_any = True
 
-                # ATC M-codes (M100/M102/M103). Each ATC M-code on the line
-                # is replaced with its (MSG,HOOK:<event>:) line and
-                # stripped from the residual.
-                atc_matches = list(_ATC_M_RE.finditer(line))
+                # ATC M-codes (M100/M102/M103). Match against the
+                # comment-stripped `code` so prose mentions like
+                # `(M102 = RELEASE)` inside a comment don't spuriously
+                # fire hooks. Each match emits a (MSG,HOOK:<event>:)
+                # line; the M-code is stripped from the executable
+                # residual but the original line's comments are kept
+                # for log readability.
+                atc_matches = list(_ATC_M_RE.finditer(code))
                 if atc_matches:
                     rewrote_any = True
                     for m in atc_matches:
@@ -359,18 +395,13 @@ class AuxPreprocessor(object):
                         event = _ATC_M_CODES.get(num)
                         if event:
                             fout.write('(MSG,HOOK:%s:)\n' % event)
-                    line = _ATC_M_RE.sub('', line)
-                    code = _PAREN_COMMENT_RE.sub('', line)
-                    code = code.split(';', 1)[0]
-                    if not code.strip():
-                        # Nothing meaningful left; preserve any trailing
-                        # comment text but skip empty lines.
-                        rest = line.rstrip()
-                        if rest:
-                            fout.write(rest + '\n')
-                        continue
-                    # Other gcode remains on the line - emit it.
-                    fout.write(line + '\n')
+                    code_stripped = _ATC_M_RE.sub('', code).strip()
+                    if code_stripped:
+                        # Mixed line: keep the residual executable
+                        # gcode. Drop the comments to keep the
+                        # rewritten file tidy (the original line's
+                        # text already appears once as the input).
+                        fout.write(code_stripped + '\n')
                     continue
 
                 # No rewrite needed.