Solution : https://service.sap.com/sap/support/notes/1310832 (SAP Service marketplace login required)
Key words : 
sap gui startup script, java parse<numbertype> methods, abap stores negative values, deeply nested type definition, java gui fails, parse<numbertype> method, native methods needed, error group jco_error_cancelled, handle close pending, stateful server connections
Related Notes : 
       
| 1385673 | SAP Java Connector Release 3.0.3 | 
| 1312880 | Security Note: clear text password in trace file | 
| 1298438 | Hanging JCo threads | 
| 1264236 | SAP Java Connector Release 3.0.1 | 
| 1077727 | SAP JCo 3.0 release and support strategy |