Eric,

Can you define the condition of the missing rows better?  That might give a
clue.

One suggestion is to compare the collations of the SQL 2000 server and
database with the collations of the SQL 2005 server and database.  If that
is a problem, you might be able to resolve it with a COLLATE clause in the
query.

RLF

Here is the script to reproduce the problem

At SQL 2000 side (SP3 or SP4) :

--cleanup
--DROP TABLE MyPackagesTranslations
--DROP TABLE MyPackages
GO
USE pubs
GO
SET ANSI_NULLS, QUOTED_IDENTIFIER ON
GO
-- Create the table MyPackages,
CREATE TABLE [dbo].[MyPackages](
   [packageIncId] [int] IDENTITY(1,1) NOT FOR REPLICATION NOT NULL,
   [packageSqlId] [smallint] NOT NULL CONSTRAINT
[DF_MyPackages_packageSqlId] DEFAULT (1121),
   [packageName] [nvarchar](60) NULL,
   [isDeleted] [bit] NOT NULL CONSTRAINT
[DF_MyPackages_isDeleted_Default] DEFAULT (0x00),
   CONSTRAINT [PK_MyPackages] PRIMARY KEY CLUSTERED
   (
       [packageIncId] ASC,
       [packageSqlId] ASC
   )
)
GO
-- Create linked table MyPackagesTranslations
CREATE TABLE [dbo].[MyPackagesTranslations](
   [packageTranslationIncId] [int] IDENTITY(1,1) NOT FOR REPLICATION
NOT NULL,
   [packageTranslationSqlId] [smallint] NOT NULL CONSTRAINT
[DF_MyPackagesTranslations_packageTranslationSqlId] DEFAULT (1121),
   [packageIncId] [int] NOT NULL,
   [packageSqlId] [smallint] NOT NULL,
   [packageTranslationName] [nvarchar](60) NULL,
   CONSTRAINT [PK_MyPackagesTranslations] PRIMARY KEY CLUSTERED
   (
       [packageTranslationIncId] ASC,
       [packageTranslationSqlId] ASC
   )
)
GO
-- ... with a foreign key between them
ALTER TABLE [dbo].[MyPackagesTranslations] WITH NOCHECK ADD CONSTRAINT
[FK_MyPackagesTranslations_MyPackages]
FOREIGN KEY([packageIncId], [packageSqlId])
REFERENCES [dbo].[MyPackages] ([packageIncId], [packageSqlId])
NOT FOR REPLICATION
GO
ALTER TABLE [dbo].[MyPackagesTranslations] CHECK CONSTRAINT
[FK_MyPackagesTranslations_MyPackages]
GO

-- Insert some data with "packageSqlId = 1"
INSERT MyPackages (packageSqlId, packageName) VALUES (1, 'Foo')
INSERT MyPackages (packageSqlId, packageName) VALUES (1, 'Bar')
INSERT MyPackages (packageSqlId, packageName) VALUES (1, 'Cat')

INSERT MyPackagesTranslations (packageIncId, packageSqlId,
packageTranslationName)
SELECT packageIncId, packageSqlId, 'Translated ' + packageName
FROM dbo.MyPackages
GO

-- Now Add a CHECK CONSTRAINT for MyPackages.packageSqlId = 1121
ALTER TABLE [dbo].[MyPackages] WITH NOCHECK ADD CONSTRAINT
[CK_MyPackages] CHECK NOT FOR REPLICATION
(([packageSqlId] = 1121))
GO
ALTER TABLE [dbo].[MyPackages] CHECK CONSTRAINT [CK_MyPackages]
GO

=> And now at SQL 2005 side (SP1 or SP2)

Execute the query :
-- Now connect to another server with SQL 2005 SP1 or SP2, and launch
the remote query
-- (first verify you have a linked server)
SELECT count(*)
from <remoteserver>.pubs.dbo.MyPackages pack
INNER JOIN <remoteserver>.pubs.dbo.MyPackagesTranslations trans
ON (pack.packageIncId=trans.packageIncId and
pack.packageSqlId=trans.packageSqlId)
where pack.isDeleted=0x0
--=> returns "0" (KO) : should be "3"