The old align could be "l", matching the "l" in "tabular".
diff --git a/R/column_spec.R b/R/column_spec.R
index ae9edff..517f07f 100644
--- a/R/column_spec.R
+++ b/R/column_spec.R
@@ -230,7 +230,8 @@
 
   kable_align_new <- paste(table_info$align_vector, collapse = align_collapse)
 
-  out <- sub(kable_align_old, kable_align_new,
+  out <- sub(paste0("\\[", kable_align_old, "\\]"),
+             paste0("\\[", kable_align_new, "\\]"),
              solve_enc(kable_input),
              perl = T)