Index: src/build.c
==================================================================
--- src/build.c
+++ src/build.c
@@ -1724,14 +1724,55 @@
     wIndex += x<0 ? 1 : aCol[pIdx->aiColumn[i]].szEst;
   }
   pIdx->szIdxRow = sqlite3LogEst(wIndex*4);
 }
 
-/* Return true if value x is found any of the first nCol entries of aiCol[]
+/* Return true if column number x is any of the first nCol entries of aiCol[].
+** This is used to determine if the column number x appears in any of the
+** first nCol entries of an index.
 */
 static int hasColumn(const i16 *aiCol, int nCol, int x){
-  while( nCol-- > 0 ) if( x==*(aiCol++) ) return 1;
+  while( nCol-- > 0 ){
+    assert( aiCol[0]>=0 );
+    if( x==*(aiCol++) ){
+      return 1;
+    }
+  }
+  return 0;
+}
+
+/*
+** Return true if any of the first nKey entries of index pIdx exactly
+** match the iCol-th entry of pPk.  pPk is always a WITHOUT ROWID
+** PRIMARY KEY index.  pIdx is an index on the same table.  pIdx may
+** or may not be the same index as pPk.
+**
+** The first nKey entries of pIdx are guaranteed to be ordinary columns,
+** not a rowid or expression.
+**
+** This routine differs from hasColumn() in that both the column and the
+** collating sequence must match for this routine, but for hasColumn() only
+** the column name must match.
+*/
+static int isDupColumn(Index *pIdx, int nKey, Index *pPk, int iCol){
+  int i, j;
+  assert( nKey<=pIdx->nColumn );
+  assert( iCol<MAX(pPk->nColumn,pPk->nKeyCol) );
+  assert( pPk->idxType==SQLITE_IDXTYPE_PRIMARYKEY );
+  assert( pPk->pTable->tabFlags & TF_WithoutRowid );
+  assert( pPk->pTable==pIdx->pTable );
+  testcase( pPk==pIdx );
+  j = pPk->aiColumn[iCol];
+  assert( j!=XN_ROWID && j!=XN_EXPR );
+  for(i=0; i<nKey; i++){
+    assert( pIdx->aiColumn[i]>=0 || j>=0 );
+    if( pIdx->aiColumn[i]==j 
+     && sqlite3StrICmp(pIdx->azColl[i], pPk->azColl[iCol])==0
+    ){
+      return 1;
+    }
+  }
   return 0;
 }
 
 /* Recompute the colNotIdxed field of the Index.
 **
@@ -1833,13 +1874,14 @@
     ** Remove all redundant columns from the PRIMARY KEY.  For example, change
     ** "PRIMARY KEY(a,b,a,b,c,b,c,d)" into just "PRIMARY KEY(a,b,c,d)".  Later
     ** code assumes the PRIMARY KEY contains no repeated columns.
     */
     for(i=j=1; i<pPk->nKeyCol; i++){
-      if( hasColumn(pPk->aiColumn, j, pPk->aiColumn[i]) ){
+      if( isDupColumn(pPk, j, pPk, i) ){
         pPk->nColumn--;
       }else{
+        testcase( hasColumn(pPk->aiColumn, j, pPk->aiColumn[i]) );
         pPk->aiColumn[j++] = pPk->aiColumn[i];
       }
     }
     pPk->nKeyCol = j;
   }
@@ -1865,20 +1907,24 @@
   */
   for(pIdx=pTab->pIndex; pIdx; pIdx=pIdx->pNext){
     int n;
     if( IsPrimaryKeyIndex(pIdx) ) continue;
     for(i=n=0; i<nPk; i++){
-      if( !hasColumn(pIdx->aiColumn, pIdx->nKeyCol, pPk->aiColumn[i]) ) n++;
+      if( !isDupColumn(pIdx, pIdx->nKeyCol, pPk, i) ){
+        testcase( hasColumn(pIdx->aiColumn, pIdx->nKeyCol, pPk->aiColumn[i]) );
+        n++;
+      }
     }
     if( n==0 ){
       /* This index is a superset of the primary key */
       pIdx->nColumn = pIdx->nKeyCol;
       continue;
     }
     if( resizeIndexObject(db, pIdx, pIdx->nKeyCol+n) ) return;
     for(i=0, j=pIdx->nKeyCol; i<nPk; i++){
-      if( !hasColumn(pIdx->aiColumn, pIdx->nKeyCol, pPk->aiColumn[i]) ){
+      if( !isDupColumn(pIdx, pIdx->nKeyCol, pPk, i) ){
+        testcase( hasColumn(pIdx->aiColumn, pIdx->nKeyCol, pPk->aiColumn[i]) );
         pIdx->aiColumn[j] = pPk->aiColumn[i];
         pIdx->azColl[j] = pPk->azColl[i];
         j++;
       }
     }
@@ -3390,13 +3436,14 @@
   */
   if( pPk ){
     for(j=0; j<pPk->nKeyCol; j++){
       int x = pPk->aiColumn[j];
       assert( x>=0 );
-      if( hasColumn(pIndex->aiColumn, pIndex->nKeyCol, x) ){
+      if( isDupColumn(pIndex, pIndex->nKeyCol, pPk, j) ){
         pIndex->nColumn--; 
       }else{
+        testcase( hasColumn(pIndex->aiColumn,pIndex->nKeyCol,x) );
         pIndex->aiColumn[i] = x;
         pIndex->azColl[i] = pPk->azColl[j];
         pIndex->aSortOrder[i] = pPk->aSortOrder[j];
         i++;
       }