All email? Or just some?
On DirectAdmin systems Roundcube uses IMAP; it's just showing you what's in your main server inbox. It doesn't have it's own separate inbox.
Are you using the standard DirectAdmin exim.conf file?
Does your exim mainlog show multiple deliveries of the same email?
When you look manually at your mailbox from the shell does the email appear more than once?
Jeff
2010-10-13 06:33:41 1P5qxP-0001Ym-6J => kontakt <[email protected]> F=<[email protected]> R=virtual_user T=virtual_localdelivery S=1723
2010-10-13 06:33:41 1P5qxP-0001Ym-6J Completed
2010-10-13 06:33:41 1P5r3E-0001uS-UE => kontakt <[email protected]> F=<[email protected]> R=virtual_user T=virtual_localdelivery S=7002
2010-10-13 06:33:41 1P5r3E-0001uS-UE Completed
2010-10-13 07:33:41 1P5rzK-0003Yl-O1 => kontakt <[email protected]> F=<[email protected]> R=virtual_user T=virtual_localdelivery S=7002
2010-10-13 07:33:41 1P5rzK-0003Yl-O1 Completed
2010-10-13 07:48:41 1P5s7Z-0003iY-Vd => kontakt <[email protected]> F=<[email protected]> R=virtual_user T=virtual_localdelivery S=56433
2010-10-13 07:48:41 1P5s7Z-0003iY-Vd Completed
2010-10-13 08:33:41 1P5svQ-0005D7-1P => kontakt <[email protected]> F=<[email protected]> R=virtual_user T=virtual_localdelivery S=7002
2010-10-13 08:33:41 1P5svQ-0005D7-1P Completed
2010-10-13 08:35:00 1P5t3M-0005dI-EW <= [email protected] H=mail01.alior.pl [195.182.52.71] P=esmtps X=TLSv1:AES256-SHA:256 S=19194 id=20101013043517.CF1BCF441@$
2010-10-13 08:35:00 1P5t3M-0005dI-EW => kontakt <[email protected]> F=<[email protected]> R=virtual_user T=virtual_localdelivery S=19305
2010-10-13 08:35:00 1P5t3M-0005dI-EW Completed
2010-10-13 08:48:41 1P5t8s-0005h3-Rb => kontakt <[email protected]> F=<[email protected]> R=virtual_user T=virtual_localdelivery S=1723
2010-10-13 08:48:41 1P5t8s-0005h3-Rb Completed
2010-10-13 09:12:46 1P5tdt-0006eu-VL <= [email protected] H=tur.go2.pl [193.17.41.50] P=esmtp S=12065 id=000a01cb6a95$42e1b270$c8a51750$@pl T="RE: Strona$
2010-10-13 09:12:46 1P5tdt-0006eu-VL => kontakt <[email protected]> F=<[email protected]> R=virtual_user T=virtual_localdelivery S=12183
2010-10-13 09:12:46 1P5tdt-0006eu-VL Completed
2010-10-13 09:33:41 1P5trV-0006s3-Ku => kontakt <[email protected]> F=<[email protected]> R=virtual_user T=virtual_localdelivery S=7002
2010-10-13 09:33:41 1P5trV-0006s3-Ku Completed
2010-10-13 10:16:25 1P5udV-0000Sp-9O <= [email protected] H=localhost (194.169.126.107) [127.0.0.1] P=esmtpa A=login:[email protected] S=567 id=c50e$
2010-10-13 10:16:25 1P5udV-0000Sp-9O ** [email protected] F=<[email protected]> R=lookuphost T=remote_smtp: SMTP error from remote mail server after R$
2010-10-13 10:16:25 1P5udV-0000Su-MP <= <> R=1P5udV-0000Sp-9O U=mail P=local S=1527 T="Mail delivery failed: returning message to sender" from <> for kontak$
2010-10-13 10:16:25 1P5udV-0000Sp-9O Completed
2010-10-13 10:16:25 1P5udV-0000Su-MP => kontakt <[email protected]> F=<> R=virtual_user T=virtual_localdelivery S=1625
2010-10-13 10:16:25 1P5udV-0000Su-MP Completed
2010-10-13 10:18:41 1P5uZr-0008L0-7L => kontakt <[email protected]> F=<[email protected]> R=virtual_user T=virtual_localdelivery S=56433
2010-10-13 10:18:41 1P5uZr-0008L0-7L Completed
2010-10-13 10:22:05 1P5uiz-0001Ky-Dz <= [email protected] H=localhost (194.169.126.107) [127.0.0.1] P=esmtpa A=login:[email protected] S=567 id=36f2$
2010-10-13 10:22:06 1P5uiz-0001Ky-Dz => [email protected] F=<[email protected]> R=lookuphost T=remote_smtp S=590 H=mx.interia.pl [217.74.65.64] C="250$
2010-10-13 10:22:06 1P5uiz-0001Ky-Dz Completed
2010-10-13 10:28:04 exim 4.69 daemon started: pid=7347, -q15m, listening for SMTP on port 25 (IPv4) port 587 (IPv4)
2010-10-13 10:28:07 1P5unb-0001ZC-MJ => kontakt <[email protected]> F=<[email protected]> R=virtual_user T=virtual_localdelivery S=7002
2010-10-13 10:28:07 1P5unb-0001ZC-MJ Completed
2010-10-13 11:28:05 1P5vjh-00046V-LM => kontakt <[email protected]> F=<[email protected]> R=virtual_user T=virtual_localdelivery S=7012
2010-10-13 11:28:05 1P5vjh-00046V-LM Completed