Can't help you, but I'm having the same basic issue (or at least it looks the same). I have a column named "LENGTH" on two tables that are related (characteristic and characteristic_type). For some reason Hibernate 3.5 is leaving the table alias off the query, even though it's using the alias on other columns in the same table. It worked in the prior version.
(select list truncated) SELECT ... characteri1_.characteristic_type_id AS charact17_10_0_, characteri1_.country_code AS country18_10_0_, characteri1_.featured_dflt AS featured8_10_0_, characteri1_.group_order AS group9_10_0_, LENGTH AS length10_0_, characteri1_.lss_chart_dflt AS lss11_10_0_, characteri1_.name AS name10_0_, characteri1_.profile_chart_dflt AS profile13_10_0_, characteri1_.profile_graph_dflt AS profile14_10_0_, ... characteri4_.characteristic_type_id AS characte1_7_3_, characteri4_.row_entry_date AS row2_7_3_, characteri4_.row_modify_date AS row3_7_3_, characteri4_.row_task_id AS row4_7_3_, characteri4_.row_user_id AS row5_7_3_, LENGTH AS length7_3_, characteri4_.name AS name7_3_, characteri4_.selection_enabled AS selection8_7_3_, country5_.country_code AS country1_1_4_, country5_.row_entry_date AS row2_1_4_, .... FROM br_seed.characteristic_data characteri0_, br_seed.characteristic characteri1_, br_seed.characteristic_grp characteri2_, br_seed.crop crop3_, br_seed.characteristic_type characteri4_, br_seed.country country5_, br_seed.crop crop6_, br_seed.br_resource resourcefi7_, br_seed.crop crop8_ WHERE characteri0_.characteristic_id = characteri1_.characteristic_id(+) AND characteri0_.crop_id = characteri1_.crop_id(+) AND characteri1_.characteristic_grp_id = characteri2_.characteristic_grp_id(+) AND characteri2_.crop_id = crop3_.crop_id(+) AND characteri1_.characteristic_type_id = characteri4_.characteristic_type_id(+) AND characteri1_.country_code = country5_.country_code(+) AND characteri1_.crop_id = crop6_.crop_id(+) AND characteri1_.br_resource_id = resourcefi7_.br_resource_id(+) AND characteri0_.crop_id = crop8_.crop_id(+) AND characteri0_.crop_id = ? AND characteri0_.seed_product_id = ?
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