diff --git a/internal/check/script.go b/internal/check/script.go
index c0a82133..e0096954 100644
--- a/internal/check/script.go
+++ b/internal/check/script.go
@@ -78,12 +78,13 @@ func (s Script) Run(blk nlp.Block, _ *core.File, _ *core.Config) ([]core.Alert,
 		// don't use our custom regexp2 library, which means the offsets
 		// (`re2loc`) will be off.
 		a := core.Alert{
-			Check:    s.Name,
-			Severity: s.Level,
-			Span:     matchLoc,
-			Link:     s.Link,
-			Match:    matchText,
-			Action:   s.Action}
+			Check:          s.Name,
+			Severity:       s.Level,
+			Span:           matchLoc,
+			Link:           s.Link,
+			Match:          matchText,
+			Action:         s.Action,
+			HasByteOffsets: true}
 
 		if matchMsg, ok := match["message"].(string); ok {
 			a.Message, a.Description = formatMessages(matchMsg, s.Description, matchText)
diff --git a/internal/core/alert.go b/internal/core/alert.go
index 4ff35fac..1757276f 100644
--- a/internal/core/alert.go
+++ b/internal/core/alert.go
@@ -27,9 +27,10 @@ type Alert struct {
 	Message     string   // the output message
 	Severity    string   // 'suggestion', 'warning', or 'error'
 	Match       string   // the actual matched text
-	Line        int      // the source line
-	Limit       int      `json:"-"` // the max times to report
-	Hide        bool     `json:"-"` // should we hide this alert?
+	Line           int      // the source line
+	Limit          int      `json:"-"` // the max times to report
+	Hide           bool     `json:"-"` // should we hide this alert?
+	HasByteOffsets bool     `json:"-"` // Span holds byte offsets into the raw document
 }
 
 // FormatAlert ensures that all required fields have data.
diff --git a/internal/core/file.go b/internal/core/file.go
index 58d70d0f..a0b1d208 100755
--- a/internal/core/file.go
+++ b/internal/core/file.go
@@ -252,6 +252,32 @@ func (f *File) assignLoc(ctx string, blk nlp.Block, pad int, a Alert) (int, []in
 	return blk.Line + 1, a.Span
 }
 
+// locFromByteOffset computes a 1-based line number and a [col, col+len] span
+// from absolute byte offsets into the raw document text. This avoids the
+// text-search approach used by FindLoc/initialPosition, which can report the
+// wrong location when the matched text appears more than once.
+func locFromByteOffset(ctx string, begin, end, pad int) (int, []int) {
+	line := 1
+	lineStart := 0
+
+	for i := 0; i < begin && i < len(ctx); i++ {
+		if ctx[i] == '\n' {
+			line++
+			lineStart = i + 1
+		}
+	}
+
+	col := nlp.StrLen(ctx[lineStart:begin]) + 1 + pad
+	matchLen := nlp.StrLen(ctx[begin:end])
+
+	span := []int{col, col + matchLen - 1}
+	if span[1] <= 0 {
+		span[1] = 1
+	}
+
+	return line, span
+}
+
 // SetText updates the file's content, lines, and history.
 func (f *File) SetText(s string) {
 	f.Content = s
@@ -271,19 +297,31 @@ func (f *File) AddAlert(a Alert, blk nlp.Block, lines, pad int, lookup bool) {
 		ctx = old
 	}
 
-	// NOTE: If the `ctx` document is large (as could be the case with
-	// `scope: raw`) this is *slow*. Thus, the cap at 1k.
+	// When the alert carries byte offsets from a script rule and falls within
+	// the document, compute line:column directly from those offsets instead of
+	// performing a text search. This fixes incorrect position reporting for
+	// script rules with `scope: raw` when the matched text appears more than
+	// once.
 	//
-	// TODO: Actually fix this.
-	if len(a.Offset) == 0 && strings.Count(ctx, a.Match) > 1 && len(ctx) < 1000 {
-		a.Offset = append(a.Offset, strings.Fields(ctx[0:a.Span[0]])...)
-	}
+	// We use blk.Context (the original document) rather than ctx, which may
+	// have been modified by ChkToCtx substitutions from earlier alerts.
+	if a.HasByteOffsets && a.Span[0] >= 0 && a.Span[1] <= len(blk.Context) {
+		a.Line, a.Span = locFromByteOffset(blk.Context, a.Span[0], a.Span[1], pad)
+	} else {
+		// NOTE: If the `ctx` document is large (as could be the case with
+		// `scope: raw`) this is *slow*. Thus, the cap at 1k.
+		//
+		// TODO: Actually fix this.
+		if len(a.Offset) == 0 && strings.Count(ctx, a.Match) > 1 && len(ctx) < 1000 {
+			a.Offset = append(a.Offset, strings.Fields(ctx[0:a.Span[0]])...)
+		}
 
-	if !lookup {
-		a.Line, a.Span = f.assignLoc(ctx, blk, pad, a)
-	}
-	if (!lookup && a.Span[0] < 0) || lookup {
-		a.Line, a.Span = f.FindLoc(ctx, blk.Text, pad, lines, a)
+		if !lookup {
+			a.Line, a.Span = f.assignLoc(ctx, blk, pad, a)
+		}
+		if (!lookup && a.Span[0] < 0) || lookup {
+			a.Line, a.Span = f.FindLoc(ctx, blk.Text, pad, lines, a)
+		}
 	}
 
 	if a.Span[0] > 0 {
diff --git a/testdata/features/checks.feature b/testdata/features/checks.feature
index 22c15ecf..e170ca46 100755
--- a/testdata/features/checks.feature
+++ b/testdata/features/checks.feature
@@ -3,7 +3,7 @@ Feature: Checks
         When I test "checks/Script"
         Then the output should contain exactly:
             """
-            test.md:4:19:Scripts.CustomMsg:Some message
+            test.md:1:2:Scripts.CustomMsg:Some message
             test.md:29:1:Checks.ScriptRE:Consider inserting a new section heading at this point.
             test.md:39:1:Checks.ScriptRE:Consider inserting a new section heading at this point.
             """