After much investigation it looks like an issue with association negotiation between orthanc and conquest.
When sending from Conquest to Orthanc : Conquest lists CT once with two syntaxes, ideally the highest priority should be accepted by Orthanc but it doesnot do that and accepts the default fallback option.
When sending from Orthanc to Conquest/Radiant/Another Orthanc : Orthanc lists CT twice with different syntaxes.
Packet capture reveals the following:
Orthanc to Orthanc Request:
A-ASSOCIATE request ROUTER → ORTHANC
Protocol Version: 1
Called AE Title: ORTHANC
Calling AE Title: ROUTER
Application Context: DICOM Application Context Name (1.2.840.10008.3.1.1.1)
Presentation Context: CT Image Storage (1.2.840.10008.5.1.4.1.1.2)
Item Type: Presentation Context (0x20)
Item Length: 59
Context ID: 0x01
Abstract Syntax: CT Image Storage (1.2.840.10008.5.1.4.1.1.2)
Transfer Syntax: JPEG Lossless, Non-Hierarchical (Process 14) (1.2.840.10008.1.2.4.57)
Presentation Context: CT Image Storage (1.2.840.10008.5.1.4.1.1.2)
Item Type: Presentation Context (0x20)
Item Length: 54
Context ID: 0x03
Abstract Syntax: CT Image Storage (1.2.840.10008.5.1.4.1.1.2)
Transfer Syntax: Implicit VR Little Endian: Default Transfer Syntax for DICOM (1.2.840.10008.1.2)
Presentation Context: CT Image Storage (1.2.840.10008.5.1.4.1.1.2)
Item Type: Presentation Context (0x20)
Item Length: 56
Context ID: 0x05
Abstract Syntax: CT Image Storage (1.2.840.10008.5.1.4.1.1.2)
Transfer Syntax: Explicit VR Little Endian (1.2.840.10008.1.2.1)
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User Info: Max PDU Length 16384, Implementation UID 1.2.276.0.7230010.3.0.3.6.5, Version OFFIS_DCMTK_365
Orthanc to Orthanc Response:
A-ASSOCIATE accept ROUTER ← ORTHANC
Protocol Version: 1
Called AE Title: ORTHANC
Calling AE Title: ROUTER
Application Context: DICOM Application Context Name (1.2.840.10008.3.1.1.1)
Presentation Context: ID 0x01, Accept, JPEG Lossless, Non-Hierarchical (Process 14), CT Image Storage
Item Type: Presentation Context Reply (0x21)
Item Length: 30
Context ID: 0x01
Result: Accept (0x0)
Transfer Syntax: JPEG Lossless, Non-Hierarchical (Process 14) (1.2.840.10008.1.2.4.57)
Presentation Context: ID 0x03, Accept, Implicit VR Little Endian: Default Transfer Syntax for DICOM, CT Image Storage
Item Type: Presentation Context Reply (0x21)
Item Length: 25
Context ID: 0x03
Result: Accept (0x0)
Transfer Syntax: Implicit VR Little Endian: Default Transfer Syntax for DICOM (1.2.840.10008.1.2)
Presentation Context: ID 0x05, Accept, Explicit VR Little Endian, CT Image Storage
Item Type: Presentation Context Reply (0x21)
Item Length: 27
Context ID: 0x05
Result: Accept (0x0)
Transfer Syntax: Explicit VR Little Endian (1.2.840.10008.1.2.1)
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User Info: Max PDU Length 16384, Implementation UID 1.2.276.0.7230010.3.0.3.6.6, Version OFFIS_DCMTK_366
Conquest to Orthanc Request:
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A-ASSOCIATE request CONQUESTSRV2 → ORTHANC
Protocol Version: 1
Called AE Title: ORTHANC
Calling AE Title: CONQUESTSRV2
Application Context: DICOM Application Context Name (1.2.840.10008.3.1.1.1)
Presentation Context: CT Image Storage (1.2.840.10008.5.1.4.1.1.2)
Item Type: Presentation Context (0x20)
Item Length: 106
Context ID: 0xeb
Abstract Syntax: CT Image Storage (1.2.840.10008.5.1.4.1.1.2)
Transfer Syntax: JPEG Lossless, Non-Hierarchical (Process 14) (1.2.840.10008.1.2.4.57)
Transfer Syntax: JPEG Lossless, Non-Hierarchical, First-Order Prediction (Process 14 [Selection Value 1]): Default Transfer Syntax for Lossless JPEG Image Compression (1.2.840.10008.1.2.4.70)
Transfer Syntax: Implicit VR Little Endian: Default Transfer Syntax for DICOM (1.2.840.10008.1.2)
User Info: Max PDU Length 32768, Implementation UID 1.2.826.0.1.3680043.2.135.1066.101, Version 1.5.0/WIN32
Orthanc to Conquest Response:
A-ASSOCIATE accept CONQUESTSRV2 ← ORTHANC
Protocol Version: 1
Called AE Title: ORTHANC
Calling AE Title: CONQUESTSRV2
Application Context: DICOM Application Context Name (1.2.840.10008.3.1.1.1)
Presentation Context: ID 0xeb, Accept, Implicit VR Little Endian: Default Transfer Syntax for DICOM, CT Image Storage
Item Type: Presentation Context Reply (0x21)
Item Length: 25
Context ID: 0xeb
Result: Accept (0x0)
Transfer Syntax: Implicit VR Little Endian: Default Transfer Syntax for DICOM (1.2.840.10008.1.2)
User Info: Max PDU Length 16384, Implementation UID 1.2.276.0.7230010.3.0.3.6.6, Version OFFIS_DCMTK_366